Immune regulatory oligonucleotide (iro) compounds to modulate toll-like receptor based immune response

ABSTRACT

The invention provides novel immune regulatory oligonucleotides (IRO) as antagonist of TLRs and methods of use thereof. These IROs have unique sequences that inhibit or suppress TLR-mediated signaling in response to a TLR ligand or TLR agonist. The methods may have use in the prevention and treatment of cancer, an autoimmune disorder, airway inflammation, inflammatory disorders, infectious disease, skin disorders, allergy, asthma or a disease caused by a pathogen.

RELATED APPLICATIONS

This application is a continuation of U.S. application Ser. No.14/791,749, filed Jul. 6, 2015, which is a continuation of U.S.application Ser. No. 13/905,242, filed May 30, 2013 (now U.S. Pat. No.9,096,858), which is a continuation of U.S. application Ser. No.13/299,555, filed Nov. 18, 2011 (now U.S. Pat. No. 8,486,908), whichclaims the benefit of U.S. Provisional Application No. 61/415,494, filedon Nov. 19, 2010 and U.S. Provisional Application No. 61/511,709, filedon Jul. 26, 2011. The entire teachings of the above applications areincorporated herein by reference.

BACKGROUND OF THE INVENTION

Field of the Invention

The invention generally relates to the field of immunology andimmunotherapy, and more specifically to immune regulatoryoligonucleotide (IRO) compositions and their use for inhibition and/orsuppression of Toll-like Receptor-mediated immune responses. Inparticular, the invention relates to antagonists of Toll-Like Receptors7 (TLR7) and/or TLR9 that uniquely inhibit cytokines normally producedthrough TLR7 and/or TLR9 stimulation.

Summary of the Related Art

Toll-like receptors (TLRs) are present on many cells of the immunesystem and have been shown to be involved in the innate immune response(Hornung, V. et al., (2002) J. Immunol. 168:4531-4537). In vertebrates,or mammals, this family consists often proteins called TLR1 to TLR10,which are known to recognize pathogen associated molecular patterns frombacteria, fungi, parasites, and viruses (Poltorak, A. et al. (1998)Science 282:2085-2088; Underhill, D. M., et al. (1999) Nature401:811-815; Hayashi, F. et. al (2001) Nature 410:1099-1103; Zhang, D.et al. (2004) Science 303:1522-1526; Meier, A. et al. (2003) Cell.Microbiol. 5:561-570; Campos, M. A. et al. (2001) J. Immunol. 167:416-423; Hoebe, K. et al. (2003) Nature 424: 743-748; Lund, J. (2003) J.Exp. Med. 198:513-520; Heil, F. et al. (2004) Science 303:1526-1529;Diebold, S. S., et al. (2004) Science 303:1529-1531; Hornung, V. et al.(2004) J. Immunol. 173:5935-5943). TLRs are a key means by which mammalsrecognize and mount an immune response to foreign molecules and alsoprovide a means by which the innate and adaptive immune responses arelinked (Akira, S. et al. (2001) Nature Immunol. 2:675-680; Medzhitov, R.(2001) Nature Rev. Immunol. 1:135-145). TLRs have also been shown toplay a role in the pathogenesis of many diseases, includingautoimmunity, infectious disease, and inflammation (Cook, D. N. et al.(2004) Nature Immunol. 5:975-979) and the regulation of TLR-mediatedactivation using appropriate agents may provide a means for diseaseintervention.

Some TLRs are located on the cell surface to detect and initiate aresponse to extracellular pathogens and other TLRs are located insidethe cell to detect and initiate a response to intracellular pathogens.Table 1 provides a representation of TLRs, their cellular location, andthe known agonists therefore (Diebold, S. S. et al. (2004) Science303:1529-1531; Liew, F. et al. (2005) Nature 5:446-458; Hemmi H et al.(2002) Nat Immunol 3:196-200; Jurk M et al., (2002) Nat Immunol 3:499;Lee J et al. (2003) Proc. Natl. Acad. Sci. USA 100:6646-6651);(Alexopoulou, L. (2001) Nature 413:732-738).

TABLE 1 TLR Molecule Agonist Cell Surface TLRs: TLR2 bacteriallipopeptides TLR4 gram negative bacteria TLR5 motile bacteria TLR6 grampositive bacteria Endosomal TLRs: TLR3 double stranded RNA viruses TLR7single stranded RNA viruses TLR8 single stranded RNA viruses TLR9unmethylated DNA

Certain unmethylated CpG motifs present in bacterial and synthetic DNAhave been shown to activate the immune system and induce antitumoractivity. (Tokunaga T et al., J. Natl. Cancer Inst. (1984) 72:955-962;Shimada S, et al., Jpn. H cancer Res, 1986, 77, 808-816; Yamamoto S, etal., Jpn. J. Cancer Res., 1986, 79, 866-73). Other studies usingantisense oligonucleotides containing CpG dinucleotides have been shownto stimulate immune responses (Zhao Q, et al. (1996) Biochem. Pharmacol.26:173-182). Subsequent studies demonstrated that TLR9 recognizesunmethylated CpG motifs present in bacterial and synthetic DNA (Hemmi,H. et al. (2000) Nature 408:740-745). Other modifications ofCpG-containing phosphorothioate oligonucleotides can also affect theirability to act as modulators of immune response through TLR9 (see, e.g.,Zhao et al., Biochem. Pharmacol. (1996) 51:173-182; Zhao et al. (1996)Biochem Pharmacol. 52:1537-1544; Zhao et al. (1997) Antisense NucleicAcid Drug Dev. 7:495-502; Zhao et al (1999) Bioorg. Med. Chem. Lett.9:3453-3458; Zhao et al. (2000) Bioorg. Med. Chem. Lett. 10:1051-1054;Yu, D. et al. (2000) Bioorg. Med. Chem. Lett. 10:2585-2588; Yu, D. etal. (2001) Bioorg. Med. Chem. Lett. 11:2263-2267; and Kandimalla, E. etal. (2001) Bioorg. Med. Chem. 9:807-813). In addition, structureactivity relationship studies have allowed identification of syntheticmotifs and novel DNA-based compounds that induce specific immuneresponse profiles that are distinct from those resulting fromunmethylated CpG dinucleotides. (Kandimalla, E. et al. (2005) Proc.Natl. Acad. Sci. USA 102:6925-6930. Kandimalla, E. et al. (2003) Proc.Nat. Acad. Sci. USA 100:14303-14308; Cong, Y. et al. (2003) BiochemBiophys Res. Commun. 310:1133-1139; Kandimalla, E. et al. (2003)Biochem. Biophys. Res. Commun. 306:948-953; Kandimalla, E. et al. (2003)Nucleic Acids Res. 31:2393-2400; Yu, D. et al. (2003) Bioorg. Med. Chem.11:459-464; Bhagat, L. et al. (2003) Biochem. Biophys. Res. Commun.300:853-861; Yu, D. et al. (2002) Nucleic Acids Res. 30:4460-4469; Yu,D. et al. (2002) J. Med. Chem. 45:4540-4548. Yu, D. et al. (2002)Biochem. Biophys. Res. Commun. 297:83-90; Kandimalla. E. et al. (2002)Bioconjug. Chem. 13:966-974; Yu, D. et al. (2002) Nucleic Acids Res.30:1613-1619; Yu, D. et al. (2001) Bioorg. Med. Chem. 9:2803-2808; Yu,D. et al. (2001) Bioorg. Med. Chem. Lett. 11:2263-2267; Kandimalla, E.et al. (2001) Bioorg. Med. Chem. 9:807-813; Yu, D. et al. (2000) Bioorg.Med. Chem. Lett. 10:2585-2588; Putta, M. et al. (2006) Nucleic AcidsRes. 34:3231-3238).

The selective localization of TLRs and the signaling generatedtherefrom, provides some insight into their role in the immune response.The immune response involves both an innate and an adaptive responsebased upon the subset of cells involved in the response. For example,the T helper (Th) cells involved in classical cell-mediated functionssuch as delayed-type hypersensitivity and activation of cytotoxic Tlymphocytes (CTLs) are Th1 cells. This response is the body's innateresponse to antigen (e.g. viral infections, intracellular pathogens, andtumor cells), and results in a secretion of IFN-gamma and a concomitantactivation of CTLs. Alternatively, the Th cells involved as helper cellsfor B-cell activation are Th2 cells. Th2 cells have been shown to beactivated in response to bacteria and parasites and may mediate thebody's adaptive immune response (e.g. IgE production and eosinophilactivation) through the secretion of IL-4 and IL-5. The type of immuneresponse is influenced by the cytokines produced in response to antigenexposure and the differences in the cytokines secreted by Th1 and Th2cells may be the result of the different biological functions of thesetwo subsets.

While activation of TLRs is involved in mounting an immune response, anuncontrolled stimulation of the immune system through TLRs mayexacerbate certain diseases in immune compromised subjects. In recentyears, several groups have shown the use of syntheticoligodeoxyoligonucleotides (ODNs) as inhibitors of inflammatorycytokines (Lenert, P. et al. (2003) DNA Cell Biol. 22(10):621-631).

Using certain synthetic ODNs, Lenert et al. report the ability toproduce inhibitory ODNs (Lenert, P. et al. (2003) DNA Cell Biol.22(10):621-631). These inhibitory ODN require two triplet sequences, aproximal “CCT” triplet and a distal “GGG” triplet. In addition to thesetriplet-containing inhibitory ODNs, several groups have reported otherspecific DNA sequences that could inhibit TLR-9-mediated activation byCpG-containing ODNs. These “inhibitory” or “suppressive” motifs are richin poly “G” (e.g. “GGGG”) or “GC” sequences, tend to be methylated, andare present in the DNA of mammals and certain viruses (see e.g., Chen,Y., et al., Gene Ther. 8: 1024-1032 (2001); Stunz, L. L., Eur. J.Immunol. 32: 1212-1222 (2002). Duramad, O., et al., J. Immunol., 174:5193-5200 (2005) and Jurk et. al (US 2005/0239733), describe a structurefor inhibitory DNA oligonucleotides containing a GGGG motif within thesequences. Patole et al. demonstrate that GGGG containing ODNs willsuppress systemic lupus (Patole, P. et al. (2005) J. Am. Soc. Nephrol.16:3273-3280). Additionally, Gursel, I., et al., J. Immunol., 171:1393-1400 (2003), describe repetitive TTAGGG elements, which are presentat high frequency in mammalian telomeres, down-regulate CpG-inducedimmune activation. Shirota, H., et al., J. Immunol., 173: 5002-5007(2004), demonstrate that synthetic oligonucleotides containing theTTAGGG element mimic this activity and could be effective in theprevention/treatment of certain Th1-dependent autoimmune diseases.

In contrast, some studies have called into question the view that poly Gcontaining ODNs are acting as antagonists of TLRs. For example, U.S.Pat. No. 6,426,334, Agrawal et al., demonstrate that administering CpGoligonucleotides containing GGGG strings have potent antiviral andanticancer activity and that administration of these compounds willcause an increase in serum IL-12 concentration. Further, CpG oligoscontaining polyG sequences are known to induce immune responses throughTLR9 activation (Verthelyi D et al, J Immunol. 166, 2372, 2001; Gursel Met al, J Leukoc Biol, 71, 813, 2001, Krug A et al, Eur J Immunol, 31,2154, 2001) and show antitumor and antiviral activities (Ballas G K etal, J Immunol, 167, 4878, 2001; Verthelyi D et al, J Immunol, 170, 4717,2003). In addition, polyG oligonucleotides are known to inhibit HIV andRel A (McShan W M, et al, J Biol Chem., 267(8):5712-21, 1992; Rando, R Fet al., J Biol Chem, 270(4):1754-60, 1995; Benimetskaya L, et al.,Nucleic Acids Res., 25(13):2648-56, 1997); and ODNs containing an immunestimulatory CpG motif and 4 consecutive G nucleotides (known as class AODNs) induce interferon-γ production and a Th1 shift in the immuneresponse. Moreover, in preclinical disease models, Class A ODNs havebeen shown to induce a TLR-mediated immune response.

As an additional limitation, oligonucleotides containing guanosinestrings have been shown to form tetraplex structures, act as aptamers,and inhibit thrombin activity (Bock L C et al., Nature, 355:564-6, 1992;Padmanabhan, K et al., J Biol Chem., 268(24):17651-4, 1993). Thus, it isnot clear whether single-stranded or multiple-stranded structures areeffective at suppressing TLR9 activation.

Kandimalla et al. (Ser. No. 11/549,048) describe a novel class of TLRantagonists that do not require a polyG sequence. Kandimalla et al. alsodescribes the application of these novel compositions to treating andpreventing various diseases and disorders (Ser. No. 11/549,048;11/743,876; 12/140,334; 12/140,338; 12/244,199). However a challengeremains to develop additional TLR antagonists that do not require apolyG sequence and thus do not present the problem of forming secondarystructures. This challenge may be solved through the design of newoligonucleotide-based compounds and compositions that can act as uniqueinhibitors of TLRs 7 and/or 9. Such new custom compounds andcompositions will find use in many clinically relevant applications,including treating and preventing diseases and disorders with an immunestimulatory component.

BRIEF SUMMARY OF THE INVENTION

The inventors have surprisingly discovered that uniquely modifying thenucleic acid sequence on the 5′-side of a core immune stimulatorydinucleotide, the nucleic acids within the core immune stimulatorydinucleotide, the linkages between nucleotides or the linkers connectingtwo or more oligonucleotides produces novel antagonists of TLR7 and/orTLR9 that distinctly antagonize, inhibit, suppress or prevent the invitro and in vivo cytokine and chemokine profiles normally generatedthrough TLR7 and/or TLR9 stimulation. This ability to antagonize,inhibit suppress or prevent the cytokine and chemokine response to aTLR7 and/or TLR9 agonist provides the ability to prevent and/or treatvarious disease conditions in a disease-specific and even apatient-specific manner.

Thus, the invention provides immune regulatory oligonucleotides (IRO)compounds that act as distinct antagonists of TLR7 and/or TLR9 andmethods of using such compounds to antagonize, inhibit, suppress orprevent TLR7- and/or TLR9-mediated immune stimulation. These IROcompounds comprise an immune stimulatory motif and would be immunestimulatory but for one or more chemical modifications in the nucleicacid sequence on the 5′-side of the immune stimulatory motif and/or inthe immune stimulatory motif. The IRO compounds and compositions thatpreferentially antagonize, inhibit, suppress or prevent the activity ofTLR7 and/or TLR9 have the structure 5-N_(m)-N₃N₂N₁CGN¹N²N³-N^(m)-3′ (SEQID NO: 70), wherein CG is an oligonucleotide motif selected from CpG,C*pG, C*pG* or CpG* wherein C is cytosine, C* is a cytosine analog orderivative, G is a guanine and G* is a guanine analog or derivative;N₁-N₃, at each occurrence, is independently a nucleotide or nucleotidederivative; N¹-N³, at each occurrence, is independently a nucleotide ornucleotide derivative; N_(m) and N^(m), at each occurrence, isindependently a nucleotide, nucleotide derivative or non-nucleotidelinker; provided that at least one of N₁, N₂, and N₃ and/or C and/or Gof the oligonucleotide motif is a nucleotide derivative thatantagonizes, inhibits, suppresses or prevents the activity of theoligonucleotide motif; and further provided that the compound containsless than 4 consecutive guanosine nucleotides and preferably less than 3consecutive guanosines, wherein the immune stimulatory activity of theoligonucleotide motif is antagonized, inhibited, suppressed or preventedby the nucleotide derivative; and wherein m is a number from 0 to about30.

In some embodiments, the IRO compounds may comprise at least twooligonucleotides, wherein at least two oligonucleotides are covalentlylinked via a direct nucleotide to nucleotide linkage at their 3′ endsthrough the 3′ positions of the sugars or through a modified sugar ormodified nucleobase or via a non-nucleotide linker at their 3′ endsthrough the 3′ positions of the sugars or through a modified sugar ormodified nucleobase. In preferred aspects of this embodiment, at leastone of oligonucleotides of the IRO compound has the structure5′-N_(m)-N₃N₂N₁CGN¹N²N³-N^(m)-3′ (SEQ ID NO: 70), wherein N_(m), N₁, N₂,N₃, C, G, N¹, N², N³ and N^(m) are as described above for the generalstructure of the IRO compound. In more preferred aspects of thisembodiment, at least two of the oligonucleotides of the IRO compoundhave the structure 5′-N_(m)-N₃N₂N₁CGN¹N²N³-N^(m)-3′ (SEQ ID NO: 70),wherein N_(m), N₁, N², N³, C, G, N¹, N², N³ and N^(m) are as describedabove for the general structure of the IRO compound. Such an IROcompound may have the structure5′-N_(m)-N₃N₂N₁CGN¹N²N³-N^(m)-3′-X-3′-N^(m)-N³N²N¹GCN₁N₂N₃-N_(m)-5′(5′-SEQ ID NO: 70-3′-X-3′-SEQ ID NO: 70-5′), wherein X is a nucleotidelinkage or a non-nucleotide linker and N_(m), N₁, N₂, N₃, C, G, N¹, N²,N³ and N^(m) are as described above for the general structure of the IROcompound.

The IRO compounds and compositions according to the inventionpreferentially inhibit TLR7 and/or TLR9-mediated immune responses invarious cell types and in various in vitro and in vivo experimentalmodels, with each compound or composition providing a distinct immuneinhibition profile.

The invention further provides for a pharmaceutical compositioncomprising an IRO compound according to the invention and apharmaceutically acceptable carrier.

The invention further provides a method for inhibiting a TLR-mediatedimmune response in a vertebrate, or mammal, the method comprisingadministering to the mammal an IRO compound or composition according tothe invention in a pharmaceutically effective amount. In some preferredembodiments, suppressing or inhibiting TLR stimulation comprisesadministering an IRO compound according to the invention, wherein theTLR is selected from TLR7 and TLR9.

The invention further provides a method for suppressing or inhibitingthe activity of a TLR agonist comprising administering an IRO compoundaccording to the invention, wherein the IRO compound is administered atthe same time, prior to or after the TLR agonist. In preferredembodiments the TLR agonist is selected from agonists of TLR7 and TLR9.

The invention further provides a method for therapeutically treating avertebrate, or mammal, having a disease mediated by TLR7 and/or TLR9,such method comprising administering to the mammal an IRO compoundaccording to the invention in a pharmaceutically effective amount. Inpreferred embodiments, the disease is cancer, an autoimmune disease ordisorder, airway inflammation, an inflammatory disease or disorder,infectious disease, malaria, Lyme disease, ocular infections,conjunctivitis, skin disorders, psoriasis, scleroderma, cardiovasculardisease, atherosclerosis, chronic fatigue syndrome, sarcoidosis,transplant rejection, allergy, asthma or a disease caused by a pathogen.Preferred autoimmune diseases and disorders include without limitationlupus erythematosus, multiple sclerosis, type I diabetes mellitus,irritable bowel syndrome, Chron's disease, rheumatoid arthritis, septicshock, alopecia universalis, acute disseminated encephalomyelitis,Addison's disease, ankylosing spondylitis, antiphospholipid antibodysyndrome, autoimmune hemolytic anemia, autoimmune hepatitis, Bullouspemphigoid, chagas disease, chronic obstructive pulmonary disease,coeliac disease, dermatomyositis, endometriosis, Goodpasture's syndrome,Graves' disease, Guillain-Barre syndrome, Hashimoto's disease,hidradenitis suppurativa, idiopathic thrombocytopenic purpura,interstitial cystitis, morphea, myasthenia gravis, narcolepsy,neuromyotonia, pemphigus, pernicious anaemia, polymyositis, primarybiliary cirrhosis, schizophrenia, Sjögren's syndrome, temporal arteritis(also known as “giant cell arteritis”), vasculitis, vitiligo,vulvodynia, and Wegener's granulomatosis. Preferred inflammatorydiseases and disorders include without limitation airway inflammation,asthma, autoimmune diseases, chronic inflammation, chronic prostatitis,glomerulonephritis, Behçet's disease, hypersensitivities, inflammatorybowel disease, reperfusion injury, rheumatoid arthritis, transplantrejection, ulcerative colitis, uveitis, conjunctivitis, and vasculitis.

The invention further provides a method for preventing cancer,autoimmune diseases or disorders, airway inflammation, inflammatorydiseases or disorders, infectious disease, malaria, Lyme disease, ocularinfections, conjunctivitis, skin disorders, psoriasis, scleroderma,cardiovascular disease, atherosclerosis, chronic fatigue syndrome,sarcoidosis, transplant rejection, allergy, asthma or a disease causedby a pathogen in a vertebrate, or mammal, such method comprisingadministering to the mammal an IRO compound according to the inventionin a pharmaceutically effective amount. Preferred autoimmune diseasesand disorders include without limitation lupus erythematosus, multiplesclerosis, type I diabetes mellitus, irritable bowel syndrome, Chron'sdisease, rheumatoid arthritis, septic shock, alopecia universalis, acutedisseminated encephalomyelitis, Addison's disease, ankylosingspondylitis, antiphospholipid antibody syndrome, autoimmune hemolyticanemia, autoimmune hepatitis, Bullous pemphigoid, chagas disease,chronic obstructive pulmonary disease, coeliac disease, dermatomyositis,endometriosis, Goodpasture's syndrome, Graves' disease, Guillain-Barresyndrome, Hashimoto's disease, hidradenitis suppurativa, idiopathicthrombocytopenic purpura, interstitial cystitis, morphea, myastheniagravis, narcolepsy, neuromyotonia, pemphigus, pernicious anaemia,polymyositis, primary biliary cirrhosis, schizophrenia, Sjögren'ssyndrome, temporal arteritis (also known as “giant cell arteritis”),vasculitis, vitiligo, vulvodynia, and Wegener's granulomatosis.Preferred inflammatory diseases and disorders include without limitationairway inflammation, asthma, autoimmune diseases, chronic inflammation,chronic prostatitis, glomerulonephritis, Behçet's disease,hypersensitivities, inflammatory bowel disease, reperfusion injury,rheumatoid arthritis, transplant rejection, ulcerative colitis, uveitis,conjunctivitis, and vasculitis.

In some preferred embodiments, the IRO compound according to theinvention is administered in combination with one or more vaccines,antigens, antibodies, cytotoxic agents, allergens, antibiotics,antisense oligonucleotides, TLR agonists, TLR antagonists, peptides,proteins, gene therapy vectors, DNA vaccines, adjuvants, kinaseinhibitors or co-stimulatory molecules or combinations thereof. In somepreferred embodiments, the route of administration is parenteral,mucosal delivery, oral, sublingual, transdermal, topical, inhalation,intranasal, aerosol, intraocular, intratracheal, intrarectal,intragastric, vaginal, by gene gun, dermal patch or in eye drop ormouthwash form.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 is a synthetic scheme for the linear synthesis of immuneregulatory compounds of the invention. DMTr=4,4′-dimethoxytrityl;CE=cyanoethyl.

FIG. 2 is a synthetic scheme for the parallel synthesis of immuneregulatory oligonucleotides of the invention. DMTr=4,4′-dimethoxytrityl;CE=cyanoethyl.

FIGS. 3A-3C depicts the ability of TLR7/9 antagonists according to theinvention to inhibit TLR7-induced cytokines/chemokines by TLR7/9antagonists in mouse splenocytes treated according to Example 3.

FIGS. 4A-4C depicts the ability of TLR7/9 antagonists according to theinvention to inhibit TLR9-induced cytokines/chemokines by TLR7/9antagonists in mouse splenocytes treated according to Example 3.

FIG. 5 depicts the ability of TLR7/9 antagonists according to theinvention to inhibit TLR7-induced IL-12 in vivo in mice treatedaccording to Example 4.

FIG. 6 depicts the ability of TLR7/9 antagonists according to theinvention to inhibit TLR9-induced IL-12 in vivo in mice treatedaccording to Example 4.

FIG. 7 depicts the ability of TLR7/9 antagonists according to theinvention to inhibit TLR7-induced IL-12 in vivo over time in micetreated according to Example 4.

FIG. 8 depicts the ability of TLR7/9 antagonists according to theinvention to inhibit TLR9-induced inhibition of IL-12 in vivo over timein mice treated according to Example 4.

FIGS. 9A-9B depicts the ability of TLR7/9 antagonists according to theinvention to selectively inhibit mouse TLR7 & 9-induced cytokines invivo in mice treated according to Example 4.

FIGS. 10A-10B demonstrates that TLR 7/9 antagonists according to theinvention do not inhibit the activity of TLR3 or TLR5 in vivo in micetreated according to Example 4.

DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENTS

The present invention relates to the therapeutic use of noveloligonucleotide-based compounds as immune modulatory agents forimmunotherapy applications. The invention provides noveloligonucleotide-based compounds that provide distinct immune inhibitionprofiles through their interaction with TLR7 and/or TLR9. Specifically,the invention provides Immune Regulatory Oligonucleotide (IRO) compoundsas antagonists of toll-like receptors (TLRs) to inhibit and/or suppressa TLR-mediated immune response. These IROs have chemical modifications,and/or internucleotide linkages, and/or linkers between oligonucleotidesthat provide their inhibition or suppression of TLR7- and/orTLR9-mediated signaling in response to endogenous and/or exogenous TLRligands or agonists. The references cited herein reflect the level ofknowledge in the field and are hereby incorporated by reference in theirentirety. Any conflicts between the teachings of the cited referencesand this specification shall be resolved in favor of the latter.

The invention further provides methods for suppressing an immuneresponse caused by TLRs and can be used for immunotherapy applicationssuch as, but not limited to, treatment of cancer, autoimmune disorders,asthma, respiratory allergies, food allergies, skin allergies, systemiclupus erythematosus (SLE), arthritis, pleurisy, chronic infections,inflammatory diseases, inflammatory bowel syndrome, sepsis, andbacteria, parasitic, and viral infections in adult and pediatric humanand veterinary applications. Thus, the invention provides IRO compoundshaving optimal levels of immune modulatory effect for immunotherapy andmethods for making and using such compounds. In addition, IRO compoundsof the invention are useful in combination with, for example, vaccines,antigens, antibodies, allergens, chemotherapeutic agents (bothchemotherapy and targeted therapies), and/or antisense oligonucleotidesfor prevention and treatment of diseases.

Definitions

The term “oligonucleotide” generally refers to a polynucleosidecomprising a plurality of linked nucleoside units. Such oligonucleotidescan be obtained from existing nucleic acid sources, including genomic orcDNA, but are preferably produced by synthetic methods. In preferredembodiments each nucleoside unit can encompass various chemicalmodifications and substitutions as compared to wild-typeoligonucleotides, including but not limited to modified nucleoside baseand/or modified sugar unit. Examples of chemical modifications are knownto the person skilled in the art and are described, for example, inUhlmann E et al. (1990) Chem. Rev. 90:543; “Protocols forOligonucleotides and Analogs” Synthesis and Properties & Synthesis andAnalytical Techniques, S. Agrawal, Ed, Humana Press, Totowa, USA 1993;and Hunziker, J. et al. (1995) Mod. Syn. Methods 7:331-417; and Crooke,S. et al. (1996) Ann. Rev. Pharm. Tox. 36:107-129. The nucleosideresidues can be coupled to each other by any of the numerous knowninternucleoside linkages. Such internucleoside linkages include, withoutlimitation, phosphodiester, phosphorothioate, phosphorodithioate,alkylphosphonate, alkylphosphonothioate, phosphotriester,phosphoramidate, siloxane, carbonate, carboalkoxy, acetamidate,carbamate, morpholino, borano, thioether, bridged phosphoramidate,bridged methylene phosphonate, bridged phosphorothioate, and sulfoneintemucleoside linkages. The term “oligonucleotide” also encompassespolynucleosides having one or more stereospecific internucleosidelinkage (e.g., (R_(P))- or (S_(P))-phosphorothioate, alkylphosphonate,or phosphotriester linkages). As used herein, the terms“oligonucleotide” and “dinucleotide” are expressly intended to includepolynucleosides and dinucleosides having any such intemucleosidelinkage, whether or not the linkage comprises a phosphate group. Incertain preferred embodiments, these intemucleoside linkages may bephosphodiester, phosphorothioate or phosphorodithioate linkages orcombinations thereof.

The term “2′-substituted ribonucleoside” or “2′-substituted arabinoside”generally includes ribonucleosides or arabinonucleosides in which thehydroxyl group at the 2′ position of the pentose moiety is substitutedto produce a 2′-substituted or 2′-O-substituted ribonucleoside. Incertain embodiments, such substitution is with a lower hydrocarbyl groupcontaining 1-6 saturated or unsaturated carbon atoms, with a halogenatom, or with an aryl group having 6-10 carbon atoms, wherein suchhydrocarbyl, or aryl group may be unsubstituted or may be substituted,for example, with halo, hydroxy, trifluoromethyl, cyano, nitro, acyl,acyloxy, alkoxy, carboxyl, carboalkoxy, or amino groups. Examples of2′-O-substituted ribonucleosides or 2′-O-substituted-arabinosidesinclude, without limitation 2′-amino, 2′-fluoro, 2′-allyl, 2′-O-alkyland 2′-propargyl ribonucleosides or arabinosides,2′-O-methylribonucleosides or 2′-O-methylarabinosides and2′-O-methoxyethoxyribonucleosides or 2′-O-methoxyethoxyarabinosides.

The term “3′”, when used directionally, generally refers to a region orposition in a polynucleotide or oligonucleotide 3′ (downstream) fromanother region or position in the same polynucleotide oroligonucleotide.

The term “5′”, when used directionally, generally refers to a region orposition in a polynucleotide or oligonucleotide 5′ (upstream) fromanother region or position in the same polynucleotide oroligonucleotide.

The term “about” generally means that the exact number is not critical.Thus, the number of nucleoside residues in the oligonucleotides is notcritical, and oligonucleotides having one or two fewer nucleosideresidues, or from one to several additional nucleoside residues arecontemplated as equivalents of each of the embodiments described above.

The term “agonist” generally refers to a substance that binds to areceptor of a cell and induces a response. An agonist often mimics theaction of a naturally occurring substance such as a ligand.

The term “antagonist” generally refers to a substance that attenuates,inhibits or suppresses the effects of an agonist or ligand.

The term “adjuvant” generally refers to a substance which, when added toan immunogenic agent such as vaccine or antigen, enhances or potentiatesan immune response to the agent in the recipient host upon exposure tothe mixture.

The term “airway inflammation” generally includes, without limitation,asthma.

The term “allergen” generally refers to an antigen or antigenic portionof a molecule, usually a protein, which elicits an allergic responseupon exposure to a subject. Typically the subject is allergic to theallergen as indicated, for instance, by the wheal and flare test or anymethod known in the art. A molecule is said to be an allergen even ifonly a small subset of subjects exhibit an allergic immune response uponexposure to the molecule.

The term “allergy” generally refers to an inappropriate immune responsecharacterized by inflammation and includes, without limitation, foodallergies and respiratory allergies.

The term “antigen” generally refers to a substance that is recognizedand selectively bound by an antibody or by a T cell antigen receptor,resulting in induction of an immune response. Antigens may include butare not limited to peptides, proteins, nucleosides, nucleotides, andcombinations thereof. Antigens may be natural or synthetic and generallyinduce an immune response that is specific for that antigen.

The terms “autoimmune disease” and autoimmune disorder” generally referto diseases or disorders in which “self” components undergo attack bythe immune system.

The term “TLR-mediated disease” or TLR-mediated disorder” generallymeans any pathological condition for which activation of one or moreTLRs is a contributing factor. Such conditions include but are notlimited, cancer, autoimmune diseases or disorders, airway inflammation,inflammatory diseases or disorders, infectious diseases, skin disorders,allergy, asthma or diseases caused by a pathogen.

The term “physiologically acceptable” generally refers to a materialthat does not interfere with the effectiveness of an IRO compound orcomposition according to the invention and that is compatible with abiological system such as a cell, cell culture, tissue or organism.Preferably, the biological system is a living organism, such as avertebrate, or mammal.

The term “carrier” generally encompasses any excipient, diluent, filler,salt, buffer, stabilizer, solubilizer, oil, lipid, lipid containingvesicle, microspheres, liposomal encapsulation or other material wellknown in the art for use in pharmaceutical formulations. It will beunderstood that the characteristics of the carrier, excipient or diluentwill depend on the route of administration for a particular application.The preparation of pharmaceutically acceptable formulations containingthese materials is described in, for example, Remington's PharmaceuticalSciences, 18th Edition, ed. A. Gennaro, Mack Publishing Co., Easton,Pa., 1990.

The term “co-administration” generally refers to the administration ofat least two different substances sufficiently close in time tomodulate, suppress or inhibit an immune response. Co-administrationrefers to simultaneous administration, as well as temporally spacedorder of up to several days apart, of at least two different substancesin any order, either in a single dose or separate doses.

The term “complementary” generally means having the ability to hybridizeto a nucleic acid. Such hybridization is ordinarily the result ofhydrogen bonding between complementary strands, preferably to formWatson-Crick or Hoogsteen base pairs, although other modes of hydrogenbonding, as well as base stacking can also lead to hybridization.

The term an “effective amount” or a “sufficient amount” generally refersto an amount sufficient to affect a desired biological effect, such asbeneficial results. Thus, an “effective amount” or “sufficient amount”will depend upon the context in which it is being administered. In thecontext of administering a compound or composition that modulates animmune response to a co-administered antigen, an effective amount of anIRO compound or composition according to the invention and antigen is anamount sufficient to achieve the desired modulation, inhibition orsuppression as compared to the immune response obtained when the antigenis administered alone. An effective amount may be administered in one ormore administrations.

The term “in combination with” generally means in the course of treatinga disease or disorder in a patient, administering an IRO compound orcomposition according to the invention and an agent useful for treatingthe disease or disorder that does not diminish the immune inhibitoryeffect of the IRO compound or composition according to the invention.Such combination treatment may also include more than a singleadministration of an IRO compound or composition according to theinvention and/or independently an agent. The administration of the IROcompound or composition according to the invention and/or the agent maybe by the same or different routes.

The term “individual” or “subject” or “vertebrate” generally refers to amammal. Mammals generally include, but are not limited to, humans,non-human primates, rats, mice, cats, dogs, horses, cattle, cows, pigs,sheep, and rabbits.

The term “kinase inhibitor” generally refers to molecules thatantagonize or inhibit phosphorylation-dependent cell signaling and/orgrowth pathways in a cell. Kinase inhibitors may be naturally occurringor synthetic and include small molecules that have the potential to beadministered as oral therapeutics. Kinase inhibitors have the ability torapidly and specifically inhibit the activation of the target kinasemolecules. Protein kinases are attractive drug targets, in part becausethey regulate a wide variety of signaling and growth pathways andinclude many different proteins. As such, they have great potential inthe treatment of diseases involving kinase signaling, including cancer,cardiovascular disease, inflammatory disorders, diabetes, maculardegeneration and neurological disorders. Examples of kinase inhibitorsinclude sorafenib (NEXAVAR®), SUTENT®, dasatinib, DASATINIB™, ZACTIMA™,TYKERB™ and STI571.

The term “nucleoside” generally refers to compounds consisting of asugar, usually ribose or deoxyribose, and a purine or pyrimidine base.

The term “nucleotide” generally refers to a nucleoside comprising aphosphate group attached to the sugar.

As used herein, the term “pyrimidine nucleoside” refers to a nucleosidewherein the base component of the nucleoside is a pyrimidine base (e.g.,cytosine (C) or thymine (T) or Uracil (U)). Similarly, the term “purinenucleoside” refers to a nucleoside wherein the base component of thenucleoside is a purine base (e.g., adenine (A) or guanine (G)).

The terms “analog” or “derivative” can be used interchangeable togenerally refer to any purine and/or pyrimidine nucleotide or nucleosidethat has a modified base and/or sugar. A modified base is a base that isnot guanine, cytosine, adenine, thymine or uracil. A modified sugar isany sugar that is not ribose or 2′deoxyribose and can be used in thebackbone for an oligonucleotide.

The term “inhibiting” or “suppressing” generally refers to a decrease inor a prevention of a response or qualitative difference in a response,which could otherwise arise from eliciting and/or stimulation of aresponse.

The term “non-nucleotide linker” generally refers to any linkage ormoiety that can link or be linked to the oligonucleotides other thanthrough a phosphorous-containing linkage. Preferably such linker is fromabout 2 angstroms to about 200 angstroms in length.

The term “nucleotide linkage” generally refers to a direct 3′-5′ linkagethat directly connects the 3′ and 5′ hydroxyl groups of two nucleosidesthrough a phosphorous-containing linkage.

The terms “oligonucleotide motif” means an oligonucleotide sequence,including a dinucleotide selected from CpG, C*pG, C*pG* or CpG*. Theterms CpG, C*pG, C*pG* and CpG* refer to oligonucleotide motifs that areimmune stimulatory wherein C is cytosine, C* is a cytosine analog orderivative, G is a guanine and G* is a guanine analog or derivative.

An “oligonucleotide motif that would be immune stimulatory, but for oneor more modifications” means an oligonucleotide motif which is immunestimulatory in a parent oligonucleotide, but not in a derivativeoligonucleotide, wherein the derivative oligonucleotide is based uponthe parent oligonucleotide, but has one or more modifications. In otherwords, an “oligonucleotide motif that would be immune stimulatory, butfor one or more modifications” refers to a TLR9-inducing moiety thatwould have TLR9 agonistic activity but for that fact that it has beenfunctionally blocked or inhibited from inducing TLR9 mediated immuneresponse through modification(s) of the TLR9-inducing moiety itselfand/or by one or more chemical modification within the oligonucleotidebased compound. Modifications that inhibit the activity of aTLR9-inducing moiety include, but not limited to,2′-OMe-ribonucleosides, 3′-OMe-ribonucleosides, 3-nitropyrrole,5-nitroindole, dU, β-L-deoxynucleosides, α-deoxynucleosides, abasicnucleoside, propanediol linker, amino linker, isopropoxyl, glycerollinker, 2′-5′-DNA, 2′-5′ RNA, and P-Me DNA.

The term “treatment” generally refers to an approach intended to obtaina beneficial or desired results, which may include alleviation ofsymptoms and/or delaying and/or ameliorating the progression of adisease or disorder.

Certain IROs according to the invention are shown in Table 2. In thistable, the IRO compounds have all phosphorothioate (PS) linkages, exceptwhere indicated with ‘o’. Except where indicated, all nucleotides aredeoxyribonucleotides.

TABLE 2 IRO compound # Sequence/Structure/SEQ ID NO   15′-UGUCG1TTCT-X1-TCTTG1CUGU-5′; 5′-SEQ ID NO 1-3′-X1-3′-SED ID NO 1-5′  2 5′-UGUCG1TTC-X1-CTTG1CUGU-5′; 5′-SEQ ID NO 2-3′-X1-3′-SED ID NO 2-5′  3 5′-UGUCG1TT-X1-TTG1CUGU-5′; 5′-SEQ ID NO 3-3′-X1-3′-SED ID NO 3-5′  4 5′-UGUCoG1TTCTo-Z-oTCTTG1oCUGU-5′;5′-SEQ ID NO 4-3′-Z-3′-SED ID NO 4-5′   5 5′-GUCG1TTCTT-Z-TTCTTG1CUG-5′;5′-SEQ ID NO 5-3′-Z-3′-SED ID NO 5-5′   6 5′-UGUCG2TTCT-Z-TCTTG2CUGU-5′;5′-SEQ ID NO 6-3′-Z-3′-SED ID NO 6-5′   75′-UGUCG1TTCT-X4-TCTTG1CUGU-5′; 5′-SEQ ID NO 7-3′-X4-3′-SED ID NO 7-5′  8 5′-UGUCG1TTC-X4-CTTG1CUGU-5′; 5′-SEQ ID NO 8-3′-X4-3′-SED ID NO 8-5′  9 5′-UGUCoG1TTCTo-X4-oTCTTG1oCUGU-5′;5′-SEQ ID NO 9-3′-X4-3′-SED ID NO 9-5′  105′-GUCG1TTCTT-X4-TTCTTG1CUG-5′; 5′-SEQ ID NO 10-3′-X4-3′-SED ID NO 10-5′ 11 5′-UGUCG1TT-X4-TTG1CUGU-5′; 5′-SEQ ID NO 11-3′-X4-3′-SED ID NO 11-5′ 12 5′-UGUCG1TTC-X5-CTTG1CUGU-5′;5′-SEQ ID NO 12-3′-X5-3′-SED ID NO 12-5′  135′-UGUCG2TTC-X5-CTTG2CUGU-5′; 5′-SEQ ID NO 13-3′-X5-3′-SED ID NO 13-5′ 14 5′-UGUCG1TTC-X6-CTTG1CUGU-5′;5′-SEQ ID NO 14-3′-X6-3′-SED ID NO 14-5′  155′-UGUCG2TTC-X6-CTTG2CUGU-5′; 5′-SEQ ID NO 15-3′-X6-3′-SED ID NO 15-5′ 16 5′-UGUCG1TTCT-X7-TCTTG1CUGU-5′;5′-SEQ ID NO 16-3′-X7-3′-SED ID NO 16-5′  175′-UGUCG2TTCT-X7-TCTTG2CUGU-5′; 5′-SEQ ID NO 17-3′-X7-3′-SED ID NO 17-5′ 18 5′-UGUCG1TTC-X7-CTTG1CUGU-5′;5′-SEQ ID NO 18-3′-X7-3′-SED ID NO 18-5′  195′-TGUCG1TTCT-X-TCTTG1CUGT-5′; 5′-SEQ ID NO 19-3′-X-3′-SED ID NO 19-5′ 20 5′-CTTGUCG1TTCT-X-TCTTG1CUGTTC-5′;5′-SEQ ID NO 20-3′-X-3′-SED ID NO 20-5′  215′-TTGUCG1TTC-X-CTTG1CUGTT-5′; 5′-SEQ ID NO 21-3′-X-3′-SED ID NO 21-5′ 22 5′-CTTTGUCG1TTC-X-CTTG1CUGTTTC-5′;5′-SEQ ID NO 22-3′-X-3′-SED ID NO 22-5′  235′-TGUCG1TTCT-X7-TCTTG1CUGT-5′; 5′-SEQ ID NO 23-3′-X7-3′-SED ID NO 23-5′ 24 5′-TTGUCG1TTC-X7-CTTG1CUGTT-5′;5′-SEQ ID NO 24-3′-X7-3′-SED ID NO 24-5′  255′-GUCG1TTCTT-Z-TTCTTG1CUG-5′; 5′-SEQ ID NO 25-3′-Z-3′-SED ID NO 25-5′ 26 5′-TGUCG1TTCA-X-ACTTG1CUGT-5′;5′-SEQ ID NO 26-3′-X-3′-SED ID NO 26-5′  275′-TCTGACG1TTCT-X-TCTTG1CAGTCT-5′;5′-SEQ ID NO 27-3′-X1-3′-SED ID NO 27-5′  285′-TCTGACG2TTCT-X-TCTTG2CAGTCT-5′;5′-SEQ ID NO 28-3′-X-3′-SED ID NO 28-5′  295′-TTGUCG1TTA-X-ATTG1CUGTT-5′ 5′-SEQ ID NO 29-3′-X-3′-SED ID NO 29-5′ 30 5′-CTCTGUCG1TTA-X-ATTG1CUGTCTC-5′;5′-SEQ ID NO 30-3′-X-3′-SED ID NO 30-5′  315′-TGTC*GTTCT-X-TCTTGC*TGT-5′; 5′-SEQ ID NO 31-3′-X-3′-SED ID NO 31-5′ 32 5′-TGTCGTTCT-X-TCTTGCTGT-5′; 5′-SEQ ID NO 32-3′-X-3′-SED ID NO 32-5′ 33 5′-TGTC*GTTCT-X-TCTTGC*TGT-5′;5′-SEQ ID NO 33-3′-X-3′-SED ID NO 33-5′  34 5′-TGTCGTTCT-X-TCTTGCTGT-5′;5′-SEQ ID NO 34-3′-X-3′-SED ID NO 34-5′  355′-UGUCG1ACAT-X-TACAG1CUGU-5′; 5′-SEQ ID NO 35-3′-X-3′-SED ID NO 35-5′ 36 5′-UGUCG1TTC-X-CTTG1CUGU-5′; 5′-SEQ ID NO 36-3′-X-3′-SED ID NO 36-5′ 37 5′-UGUCG1TT-X-TTG1CUGU-5′; 5′-SEQ ID NO 37-3′-X-3′-SED ID NO 37-5′ 38 5′-UoGUCG1TToCTo-X-oTCoTTG1CUGoU-5′;5′-SEQ ID NO 38-3′-X-3′-SED ID NO 38-5′  395′-UoGoUCG1TTCTo-X-oTCTTG1CUoGoU-5′;5′-SEQ ID NO 39-3′-X-3′-SED ID NO 39-5′  405′-UGACG1TTCT-X-TCTTG1CAGU-5′; 5′-SEQ ID NO 40-3′-X-3′-SED ID NO 40-5′ 41 5′-UGUCG1ACAT-Z-TACAG1CUGU-5′;5′-SEQ ID NO 41-3′-Z-3′-SED ID NO 41-5′  425′-UGUCG1TTCT-Z-TCTTG1CUGU-5′; 5′-SEQ ID NO 42-3′-Z-3′-SED ID NO 42-5′ 43 5′-UGUCG1TTC-Z-CTTG1CUGU-5′; 5′-SEQ ID NO 43-3′-Z-3′-SED ID NO 43-5′ 44 5′-UGUCG1TT-Z-TTG1CUGU-5′; 5′-SEQ ID NO 44-3′-Z-3′-SED ID NO 44-5′ 45 5′-UGUC*GTTCT-X-TCTTGC*UGU-5′;5′-SEQ ID NO 45-3′-X-3′-SED ID NO 45-5′  46 5′-T{circumflex over( )}G{circumflex over ( )}T{circumflex over( )}C*GTTCT-X-TCTTGC*T{circumflex over ( )}G{circumflex over( )}T{circumflex over ( )}-5′; 5′-SEQ ID NO 46-3′-X-3′-SED ID NO 46-5′ 47 5′-UGUC*GTTCT-X-TCTTGC*UGU-5′;5′-SEQ ID NO 47-3′-X-3′-SED ID NO 47-5′  48 5′-T{circumflex over( )}G{circumflex over ( )}T{circumflex over( )}C*GTTCT-X-TCTTGC*-T{circumflex over ( )}G{circumflex over( )}T{circumflex over ( )}5′; 5′-SEQ ID NO 48-3′-X-3′-SED ID NO 48-5′ 49 5′-UGUCG1ACAT-X1-TACAG1CUGU-5′;5′-SEQ ID NO 49-3′-X1-3′-SED ID NO 49-5′  505′-UGACG2TTCT-X-TCTTG2CAGU-5′; 5′-SEQ ID NO 50-3′-X-3′-SED ID NO 50-5′ 51 5′-TCTGUCG1TTCT-X-TCTTG1CUGTCT-5′;5′-SEQ ID NO 51-3 ′-X-3 ′-SED ID NO 51-5′  525′-TCTGUCG2TTCT-X-TCTTG2CUGTCT-5′;5′-SEQ ID NO 52-3′-X-3′-SED ID NO 52-5′  535′-UGUCG2TTCT-X-TCTTG2CUGU-5′; 5′-SEQ ID NO 53-3′-X-3′-SED ID NO 53-5′ 54 5′-UGUCG2TT-Z-TTG2CUGU-5′; 5′-SEQ ID NO 54-3′-Z-3′-SED ID NO 54-5′ 55 5′-TUGUCG1TTC-Z-CTTG1CUGUT-5′;5′-SEQ ID NO 55-3′-Z-3′-SED ID NO 55-5′  565′-CTUGUCG1TT-Z-TTG1CUGUTC-5′; 5′-SEQ ID NO 56-3′-Z-3′-SED ID NO 56-5′ 57 5′-UCG1TTCTTC-Z-CTTCTTG1CU-5′;5′-SEQ ID NO 57-3′-Z-3′-SED ID NO 57-5′  58 5′-CTATCTGAC*GTTCTCTGT-3′;5′-SEQ ID NO 58-3′  59 5′-CTATCTGACGTTCTCTGT-3′; 5′-SEQ ID NO 59-3′  605′-CTATCTGAC*GTTCTCTGT-3′; 5′-SEQ ID NO 60-3′  615′-CTATCTGACGTTCTCTGT-3′; 5′-SEQ ID NO 61-3′  62 5′-CTATCTG{circumflexover ( )}A{circumflex over ( )}CGTTCTCTGT-3′; 5′-SEQ ID NO 62-3′  635′-CTATCTGUC*GTTCTCTGT-3′; 5′-SEQ ID NO 63-3′  645′-CTATCTGUCGTTCTCTGT-3′; 5′-SEQ ID NO 64-3′  655′-CTATCTGUC*GTTCTCTGT-3′; 5′-SEQ ID NO 65-3′  665′-CTATCTGUCGTTCTCTGT-3′; 5′-SEQ ID NO 66-3′  675′-CTTGUC*G1TTCT-X-TCTTG1C*UGTTC-5′5′-SEQ ID NO 67-3′-X-3′-SED ID NO 67-5′  68 5′-CTATCTGUC*G1TTCTCTGU-3′5′-SEQ ID NO 68-3′  69 5′-UGUCG1TTCT-X-TCTTG1CUGU-5′5′-SEQ ID NO 69-3′-X-3′-SED ID NO 69-5′  705′-TGUC*G1TTCT-X-TCTTG1C*UGT-5′ 5′-SEQ ID NO 70-3′-X-3′-SED ID NO 70-5′ 71 5′-CTTTGUC*G1TTC-X-CTTG1C*UGTTTC-5′5′-SEQ ID NO 71-3′-X-3′-SED ID NO 71-5′  725′-GUC*G1TTCTT-X-TTCTTG1C*UG-5′ 5′-SEQ ID NO 72-3′-X-3′-SED ID NO 72-5′ 73 5′-TGUC*G1TTCA-X-ACTTG1C*UGT-5′5′-SEQ ID NO 73-3′-X-3′-SED ID NO 73-5′  745′-CTTGUC*G1TTCT-X1-TCTTG1C*UGTTC-5′5′-SEQ ID NO 74-3′-X1-3′-SED ID NO 74-5′  755′-CTTGUC*G2TTCT-X-TCTTG2C*UGTTC-5′5′-SEQ ID NO 75-3′-X-3′-SED ID NO 75-5′  765′-CTTGUC*G1TTC-X5-CTTG1C*UGTTC-5′5′-SEQ ID NO 76-3′-X5-3′-SED ID NO 76-5′  775′-CTTGUC*G1TTCT-X7-TCTTG1C*UGTTC-5′5′-SEQ ID NO 77-3′-X7-3′-SED ID NO 77-5′  785′-CTTTGUC*oG1TTC-X-CTTG1oC*UGTTTC-5′5′-SEQ ID NO 78-3′-X-3′-SED ID NO 78-5′  795′-CTTTGoUC*oG1TTC-X-CTTG1oC*UoGTTTC-5′5′-SEQ ID NO 79-3′-X-3′-SED ID NO 79-5′  805′-CTTGUC*oG1TTCT-X-TCTTG1oC*UGTTC-5′5′-SEQ ID NO 80-3′-X-3′-SED ID NO 80-5′  815′-CTTGoUC*oG1TTCT-X-TCTTG1oC*UoGTTC-5′5′-SEQ ID NO 81-3′-X-3′-SED ID NO 81-5′  825′-CTGUC*oG1TTCTT-X-TTCTTG1oC*UGTC-5′5′-SEQ ID NO 82-3′-X-3′-SED ID NO 82-5′  835′-CTGoUC*oG1TTCTT-X-TTCTTG1oC*UoGTC-5′5′-SEQ ID NO 83-3′-X-3′-SED ID NO 83-5′  845′-UGUC*G1TTCT-X1-TCTTG1C*UGU-5′5′-SEQ ID NO 84-3′-X1-3′-SED ID NO 84-5′  855′-UGUC*G2TTCT-X-TCTTG2C*UGU-5′ 5′-SEQ ID NO 85-3′-X-3′-SED ID NO 85-5′ 86 5′-UGUC*G1TTC-X5-CTTG1C*UGU-5′5′-SEQ ID NO 86-3′-X5-3′-SED ID NO 86-5′  875′-UGUC*G1TTCT-X7-TCTTG1C*UGU-5′5′-SEQ ID NO 87-3′-X7-3′-SED ID NO 87-5′  88 5′-CTATCTGUC*G1TTCTCTGT-3′5′-SEQ ID NO 88-3′  89 5′-CTATCTGUC*G1TTCTCTGT-3′ 5′-SEQ ID NO 89-3′  905′-TGAC*G1TTCT-X-TCTTG1C*AGT-5′ 5′-SEQ ID NO 90-3′-X-3′-SEQ ID NO 90-5′ 91 5′-CTTGAC*G1TTCT-X-TCTTG1C*AGTTC-5′5′-SEQ ID NO 91-3′-X-3′-SED ID NO 91-5′  925′-CTTTGAC*G1TTC-X-CTTG1C*AGTTTC-5′5′-SEQ ID NO 92-3′-X-3′-SED ID NO 92-5′  935′-GAC*G1TTCTT-X-TTCTTG1C*AG-5′ 5′-SEQ ID NO 93-3′-X-3′-SED ID NO 93-5′ 94 5′-TGAC*G1TTCA-X-ACTTG1C* AGT-5′5′-SEQ ID NO 94-3′-X-3′-SED ID NO 94-5′  955′-CTTGAC*G1TTCT-X1-TCTTG1C*AGTTC-5′5′-SEQ ID NO 95-3′-X1-3′-SED ID NO 95-5′  965′-CTTGAC*G2TTCT-X-TCTTG2C*AGTTC-5′5′-SEQ ID NO 96-3′-X-3′-SED ID NO 96-5′  975′-CTTGAC*G1TTC-X5-CTTG1C*AGTTC-5′5′-SEQ ID NO 97-3′-X5-3′-SED ID NO 97-5′  985′-CTTGAC*G1TTCT-X7-TCTTG1C*AGTTC-5′5′-SEQ ID NO 98-3′-X7-3′-SED ID NO 98-5′  995′-CTTTGAC*oG1TTC-X-CTTG1oC*AGTTTC-5′5′-SEQ ID NO 99-3′-X-3′-SED ID NO 99-5′ 1005′-CTTTGoAC*oG1TTC-X-CTTG1oC*AoGTTTC-5′5′-SEQ ID NO 100-3′-X-3′-SED ID NO 100-5′ 1015′-CTTGAC*oG1TTCT-X-TCTTG1oC*AGTTC-5′5′-SEQ ID NO 101-3′-X-3′-SED ID NO 101-5′ 1025′-CTTGoAC*oG1TTCT-X-TCTTG1oC*AoGTTC-5′5′-SEQ ID NO 102-3′-X-3′-SED ID NO 102-5′ 1035′-CTGAC*oG1TTCTT-X-TTCTTG1oC*AGTC-5′5′-SEQ ID NO 103-3′-X-3′-SED ID NO 103-5′ 1045′-CTGoAC*oG1TTCTT-X-TTCTTG1oC*AoGTC-5′5′-SEQ ID NO 104-3′-X-3′-SED ID NO 104-5′ 1055′-UGAC*G1TTCT-X-TCTTG1C*AGU-5′5′-SEQ ID NO 105-3′-X-3′-SED ID NO 105-5′ 1065′-UGAC*G1TTCT-X1-TCTTG1C*AGU-5′ 5′-SEQ ID NO 106-3′-X1-3′-SED ID NO106-5′ 107 5′-UGAC*G2TTCT-X-TCTTG2C*AGU-5′5′-SEQ ID NO 107-3′-X-3′-SED ID NO 107-5′ 1085′-UGAC*G1TTC-X5-CTTG1C*AGU-5′ 5′-SEQ ID NO 108-3′-X5-3′-SED ID NO108-5′ 109 5′-UGAC*G1TTCT-X7-TCTTG1C*AGU-5′5′-SEQ ID NO 109-3′-X7-3′-SED ID NO 109-5′ 1105′-CTATCTGAC*G1TTCTCTGT-3′ 5′-SEQ ID NO 110-3′ 1115′-CTATCTGAC*G1TTCTCTGT-3′ 5′-SEQ ID NO 111-3′ 1125′-CTATCTGAC*G1TTCTCTGU-3′ 5′-SEQ ID NO 112-3′G1=7-deaza-dG; G2=AraG; C*=5-Me-dC; C*=2′-O-Me-5-Me-C;Â/Ĝ/T̂/Ĝ=2′-O-(2-methoxyethyl)-ribonucelotides; X=Glycerol Linker (alsoknown as 1,2,3-Propanetriol Linker); X1=1,2,4-Butanetriol Linker;Z=1,3,5-Pentanetriol Linker; X4=3-Trimethylamino-1, 2-propanediolLinker; X5=Bis-1,5-O-(3′-thymidyl)-1,3,5-pentanetriol Linker;X6=Bis-1,5-O-[3′-(1,2-dideoxy-D-ribosyl)]-1,3-5-pentanetriol Linker;X7=3-(2-Hydroxyethyl)-1,5-pentanediol Linker;G/U/A/C=2′-O-Me-ribonucleotides; o=Phosphodiester linkage.

In a first aspect, the invention provides immune regulatoryoligonucleotide (IRO) compounds. The term “IRO” refers to an immuneregulatory oligonucleotide-based compound that is an antagonist forTLR7- and/or TLR9, wherein the compound comprises an oligonucleotidemotif and at least one modification, wherein the oligonucleotide motifwould be immune stimulatory but for the one or more modifications thatfunctionally block or inhibit the activity of the oligonucleotide motif,provided that the compound contains less than 4 consecutive guanosinenucleotides and preferably less than 3 consecutive guanosinenucleotides. Such modifications may be in the oligonucleotide 5′terminus, in the 5′ sequence flanking the oligonucleotide motif, and/orwithin the immune stimulatory oligonucleotide motif. These modificationsresult in an IRO compound that antagonize, inhibit, suppresses orprevent TLR7- and/or TLR9-mediated immune stimulation. Suchmodifications can be to the bases, sugar residues and/or the phosphatebackbone of the nucleotides/nucleosides flanking the immune stimulatoryoligonucleotide motif or within such oligonucleotide motif.

The general structure of the IRO compound has the structure5′-N_(m)-N₃N₂N₁CGN¹N²N³-N^(m)-3′ (SEQ ID NO: 70) wherein CG is anoligonucleotide motif selected from CpG, C*pG, C*pG* or CpG* wherein Cis cytosine, C* is a cytosine analog or derivative, G is a guanine andG* is a guanine analog or derivative; N₁-N₃, at each occurrence, isindependently a nucleotide or nucleotide derivative; N¹-N³, at eachoccurrence, is independently a nucleotide or nucleotide derivative;N_(m) and N^(m), at each occurrence, is independently a nucleotide,nucleotide derivative or non-nucleotide linker; provided that at leastone of N₁, N₂, and N₃ and/or C and/or G of the oligonucleotide motif isa nucleotide derivative that functionally blocks or inhibits theactivity of the oligonucleotide motif, and further provided that thecompound contains less than 4 consecutive guanosine nucleotides andpreferably less than 3 consecutive guanosines, wherein the immunestimulatory activity of the oligonucleotide motif is antagonized,inhibited, suppressed or prevented by the nucleotide derivative; andwherein m is a number from 0 to about 30.

In preferred embodiments, N₁ is a nucleotide derivative thatfunctionally blocks or inhibits the activity of the oligonucleotidemotif. In preferred embodiments N₁ and N₂, or N₁ and N₃, or N₂ and N₃,or N₁, N₂ and N₃ are nucleotide derivatives that functionally blocks orinhibits the activity of the oligonucleotide motif.

In preferred embodiments the IRO compound is not an antisenseoligonucleotide.

In certain embodiments of the invention, the IRO compound may compriseat least two oligonucleotides (for example 2, 3, 4, 5 or 6oligonucleotides), wherein at least two oligonucleotides are covalentlylinked via a direct nucleotide to nucleotide linkage at their 3′ endsthrough the 3′ positions of the sugars or through a modified sugar ormodified nucleobase or via a non-nucleotide linker at their 3′ endsthrough the 3′ positions of the sugars or through a modified sugar ormodified nucleobase. In preferred aspects of this embodiment, at leastone of oligonucleotides of the IRO compound has the structure5′-N_(m)-N₃N₂N₁CGN¹N²N³-N^(m)-3′ (SEQ ID NO: 70), wherein N_(m), N₁, N₂,N₃, C, G, N¹, N², N³ and N^(m) are as described above for the generalstructure of the IRO compound. In more preferred aspects of thisembodiment, at least two of the oligonucleotides of the IRO compoundhave the structure 5′-N_(m)-N₃N₂N₁CGN¹N²N³-N^(m)-3′ (SEQ ID NO: 70),wherein N_(m), N₁, N₂, N₃, C, G, N¹, N², N³ and N^(m) are as describedabove for the general structure of the IRO compound. Such an IROcompound may have the structure5′-N_(m)-N₃N₂N₁CGN¹N²N³-N^(m)-3′-X-3′-N^(m)-N³N²N¹GCN₁N₂N₃-N_(m)-5′(5′-SEQ ID NO: 70-3′-X-3′-SEQ ID NO: 70-5′), wherein X is a nucleotidelinkage or a non-nucleotide linker and N_(m), N₁, N₂, N₃, C, G, N¹, N²,N³ and N^(m) are as described above for the general structure of the IROcompound.

In certain embodiments of the invention, the IRO compound that is anantagonist of TLR7 and/or TLR9 has the structure5-N_(p)N₃N₂N₁C*G*N¹N²N³N^(z)N⁴N⁵-3′ (SEQ ID NO: 71), wherein C*G* is anoligonucleotide motif wherein C* is 5-Me-dC, and G* is 7-deaza-dG;N₁-N₂, at each occurrence, is independently a 2′-O-Me-ribonucleotide;N₃, at each occurrence, is independently a nucleotide or nucleotidederivative; N¹-N³, at each occurrence, is independently a nucleotide ornucleotide derivative; N_(p) and N^(z), at each occurrence, isindependently a nucleotide or nucleotide derivative; N⁴-N⁵, at eachoccurrence, is independently a 2′-O-Me-ribonucleotide; p is a numberfrom 0 to about 30 and z is a number from 0 to about 30; provided thatthe compound contains less than 3 consecutive guanosines. In certainembodiments p and z are independently a number from 1 to about 20. Incertain embodiments p and z are independently a number from 2 to about15. In certain embodiments p and z are independently a number from 3 toabout 10.

In certain embodiments of the invention, the IRO compound that is anantagonist of TLR7 and/or TLR9 has the structure5-N_(p)N₃N₂N₁C*G*N¹N²N³N^(z)N⁴N⁵-3′ (SEQ ID NO: 72), wherein C*G* is anoligonucleotide motif wherein C* is 5-Me-dC, and G* is 7-deaza-dG;N₁-N₂, at each occurrence, is independently a 2′-O-Me-ribonucleotide;N₃, at each occurrence, is independently a nucleotide; N¹-N³, at eachoccurrence, is independently a nucleotide; N_(p) and N^(z), at eachoccurrence, is independently a nucleotide; N⁴-N⁵ at each occurrence, isindependently a 2′-O-Me-ribonucleotide; p is 5 and z is 3; provided thatthe compound contains less than 3 consecutive guanosines. Alternatively,SEQ ID NO: 72 can be written as 5′-NNNNNN₃N₂N₁C*G*N¹N²N³NNNN⁴N⁵-3′.

In preferred embodiments, two oligonucleotides having the structure5′-N_(m)-N₃N₂N₁CGN¹N²N³-N^(m)-3′ (SEQ ID NO: 70) are covalently linkedvia a direct nucleotide to nucleotide linkage at their 3′ ends throughthe 3′ positions of the sugars or through a modified sugar or modifiednucleobase or via a non-nucleotide linker at their 3′ ends through the3′ positions of the sugars or through a modified sugar or modifiednucleobase. In preferred aspects of this embodiment, the IRO compoundhas the structure5′-N_(m)-N₃N₂N₁CGN¹N²N³-N^(m)-3′-X-3′-N^(m)-N³N²N¹GCN₁N₂N₃-N_(m)-5′(5′-SEQ ID NO: 70-3′-X-3′-SEQ ID NO: 70-5′), wherein X is a nucleotidelinkage or a non-nucleotide linker and N_(m), N₁, N₂, N₃, C, G, N¹, N²,N³ and N^(m) are as described above for the general structure of the IROcompound. In preferred embodiments, the two oligonucleotides arecovalently linked directly via a nucleotide linkage. In more preferredembodiments, the two oligonucleotides are covalently linked via anon-nucleotide linker.

As a non-limiting example, the non-nucleotide linker covalently linkingthe two oligonucleotides may be attached to the 3′-hydroxyl of thesugar. In such embodiments, the linker comprises a functional group,which is attached to the 3′-hydroxyl by means of a phosphate-basedlinkage like, for example, phosphodiester, phosphorothioate,phosphorodithioate, methylphosphonate, or by a non-phosphate-basedlinkage. Possible sites of conjugation for the linker to the 3′ end ofthe oligonucleotide are indicated in Formula I, below, wherein Brepresents a heterocyclic base and wherein the arrow pointing to Pindicates any attachment to phosphorous.

In certain embodiments according to this aspect of the invention, thenon-nucleotide linker is a small molecule, macromolecule or biomolecule,including, without limitation, polypeptides, antibodies, lipids,antigens, allergens, and oligosaccharides. In certain other embodiments,the non-nucleotide linker is a small molecule. For purposes of theinvention, a small molecule is an organic moiety having a molecularweight of less than 1,000 Da. In some embodiments, the small moleculehas a molecular weight of less than 750 Da.

In some embodiments, the small molecule is an aliphatic or aromatichydrocarbon, either of which optionally can include, either in thelinear chain connecting the oligonucleotides or appended to it, one ormore functional groups including, but not limited to, hydroxy, amino,thiol, thioether, ether, amide, thioamide, ester, urea, or thiourea. Thesmall molecule can be cyclic or acyclic. Examples of small moleculelinkers include, but are not limited to, amino acids, carbohydrates,cyclodextrins, adamantane, cholesterol, haptens, and antibiotics.However, for purposes of describing the non-nucleotide linker, the term“small molecule” is not intended to include a nucleoside.

In some embodiments, the non-nucleotide linker is an alkyl linker oramino linker. The alkyl linker may be branched or unbranched, cyclic oracyclic, substituted or unsubstituted, saturated or unsaturated, chiral,achiral or racemic mixture. The alkyl linkers can have from about 2 toabout 18 carbon atoms. In some embodiments such alkyl linkers have fromabout 2 to about 9 carbon atoms. In other embodiments, the alkyl linkerhas less than 3 carbon atoms. In further embodiments, the alkyl linkerhas at least 3 carbon atoms and preferentially more than three carbonatoms. Some alkyl linkers include one or more functional groupsincluding, but not limited to, hydroxy, amino, thiol, thioether, ether,amide, thioamide, ester, urea, and thioether. Such alkyl linkers caninclude, but are not limited to, 1,2 propanediol, 1,2,3 propanetriol,1,3 propanediol, 1,2,4-Butanetriol, 1,3,5-Pentanetriol,3-trimethylamino-1,2-propanediol,Bis-1,5-O-(3′thymidyl(-1,3,5-pentanetriol,Bis-1,5-O-[3′-(1,2-dideoxy-D-robosyl)]-1,3,5-pentanetriol,3-(2-Hydroxyethyl)-1,5-pentanediol, triethylene glycol hexaethyleneglycol, polyethylene glycol linkers (e.g. [—O—CH2-CH2-]n (n=1-9)),methyl linkers, ethyl linkers, propyl linkers, butyl linkers or hexyllinkers. In some embodiments, such alkyl linkers may include peptides oramino acids.

In some embodiments, the non-nucleotide linker may include, but are notlimited to, those listed in Table 3.

TABLE 3 Representative Non-Nucleotidic Linkers

1,2,3-Propanediol linker (glycerol)

1,2,4-Butanetriol Linker

1,3,5-Pentanetriol Linker

3-Trimethylamino-1,2-propanediol Linker

Bis-1,5-O-(3′-thymidyl)-1,3,5-pentanetriol Linker

Bis-1,5-O-[3′-(1,2-dideoxy-D-ribosyl)]-1,3-5- pentanetriol Linker

3-(2-Hydroxyethyl)-1,5-pentanediol Linker

In some embodiments, the small molecule linker is glycerol or a glycerolhomolog of the formula HO—(CH₂)_(o)—CH(OH)—(CH₂)_(p)—OH, wherein o and pindependently are integers from 1 to about 6, from 1 to about 4, or from1 to about 3. In some other embodiments, the small molecule linker is aderivative of 1,3-diamino-2-hydroxypropane. Some such derivatives havethe formula HO—(CH₂)_(m)—C(O)NH—CH₂—CH(OH)—CH₂-NHC(O)—(CH₂)_(m)—OH,wherein m is an integer from 0 to about 10, from 0 to about 6, from 2 toabout 6, or from 2 to about 4.

Some non-nucleotide linkers according to the invention permit attachmentof more than two oligonucleotides. For example, the small moleculelinker glycerol has three hydroxyl groups to which oligonucleotides maybe covalently attached. Some IROs according to the invention, therefore,comprise two or more oligonucleotides linked to a nucleotide or anon-nucleotide linker. Such IROs are referred to as being “branched”.

IRO compounds also may comprise at least two oligonucleotidesnon-covalently linked, such as by electrostatic interactions,hydrophobic interactions, 7-stacking interactions, hydrogen bonding andcombinations thereof. Non-limiting examples of such non-covalent linkageincludes Watson-Crick base pairing, Hoogsteen base pairing and basestacking.

In preferred embodiments one of the oligonucleotides of the IRO compoundis not an antisense oligonucleotide. In more preferred embodimentsneither of the oligonucleotides of the IRO compound is an antisenseoligonucleotide.

In certain embodiments, pyrimidine nucleosides in the immune regulatoryoligonucleotides used in the compositions and methods according to theinvention have the structure (II):

wherein:

D is a hydrogen bond donor;

D′ is selected from the group consisting of hydrogen, hydrogen bonddonor, hydrogen bond acceptor, hydrophilic group, hydrophobic group,electron withdrawing group and electron donating group;

A is a hydrogen bond acceptor or a hydrophilic group;

A′ is selected from the group consisting of hydrogen bond acceptor,hydrophilic group, hydrophobic group, electron withdrawing group andelectron donating group;

X is carbon or nitrogen; and

S′ is a pentose or hexose sugar ring, or a sugar analog.

In certain embodiments, the sugar ring is derivatized with a phosphatemoiety, modified phosphate moiety, or other linker moiety suitable forlinking the pyrimidine nucleoside to another nucleoside or nucleosideanalog.

In some embodiments hydrogen bond donors include, without limitation,—NH—, —NH₂, —SH and —OH. Preferred hydrogen bond acceptors include,without limitation, C═O, C═S, and the ring nitrogen atoms of an aromaticheterocycle, e.g., N3 of cytosine.

In some embodiments, structure (II) is a pyrimidine nucleosidederivative. Examples of pyrimidine nucleoside derivatives include,without limitation, 5-hydroxycytosine, 5-hydroxymethylcytosine,N4-alkylcytosine, or N4-ethylcytosine, araC, 5-OH-dC, N3-Me-dC,2′-O-Me-C, 2′-O-Me-U, 2′-O-Me-T, and 4-thiouracil. Chemical modifiedderivatives also include, but are not limited to, thymine or uracilanalogues. In some embodiments, the sugar moiety S′ in (II) is a sugarderivative. Suitable sugar derivatives include, but are not limited to,trehalose or trehalose derivatives, hexose or hexose derivatives,arabinose or arabinose derivatives.

In some embodiments, the purine nucleosides in immune regulatoryoligonucleotides used in the compositions and methods according to theinvention have the structure (III):

wherein:

D is a hydrogen bond donor;

D′ is selected from the group consisting of hydrogen, hydrogen bonddonor, and hydrophilic group;

A is a hydrogen bond acceptor or a hydrophilic group;

X is carbon or nitrogen;

each L is independently selected from the group consisting of C, O, Nand S; and

S′ is a pentose or hexose sugar ring, or a sugar analog.

In certain embodiments, the sugar ring is derivatized with a phosphatemoiety, modified phosphate moiety, or other linker moiety suitable forlinking the pyrimidine nucleoside to another nucleoside or nucleosideanalog.

In certain embodiments hydrogen bond donors include, without limitation,—NH—, —NH₂, —SH and —OH. In certain embodiments hydrogen bond acceptorsinclude, without limitation, C═O, C═S, —NO₂ and the ring nitrogen atomsof an aromatic heterocycle, e.g., N1 of guanine.

In some embodiments, structure (III) is a purine nucleoside derivative.Examples of purine nucleoside derivatives include, without limitation,guanine analogues such as 7-deaza-G, 7-deaza-dG, ara-G, 6-thio-G,Inosine, Iso-G, loxoribine, TOG(7-thio-8-oxo)-G, 8-bromo-G, 8-hydroxy-G,5-aminoformycin B, Oxoformycin, 7-methyl-G, 9-p-chlorophenyl-8-aza-G,9-phenyl-G, 9-hexyl-guanine, 7-deaza-9-benzyl-G,6-Chloro-7-deazaguanine, 6-methoxy-7-deazaguanine, 8-Aza-7-deaza-G(PPG),2-(Dimethylamino)guanosine, 7-Methyl-6-thioguanosine,8-Benzyloxyguanosine, 9-Deazaguanosine,1-(B-D-ribofuranosyl)-2-oxo-7-deaza-8-methyl-purine,1-(2′-deoxy-β-D-ribofuranosyl)-2-oxo-7-deaza-8-methyl-purine,2′-O-methyl-G, and N1-Me-dG. Chemically modified derivatives alsoinclude, but are not limited to, adenine analogues such as9-benzyl-8-hydroxy-2-(2-methoxyethoxy)adenine, 2-Amino-N2-O—,methyladenosine, 8-Aza-7-deaza-A, 7-deaza-A, Vidarabine,2-Aminoadenosine, N1-Methyladenosine, 8-Azaadenosine, 5-Iodotubercidin,and 2′-O-Me-A. In some embodiments, the sugar moiety S′ in (III) is asugar derivative as defined for Formula II.

In certain embodiments of the invention, the immune regulatory nucleicacid comprises a nucleic acid sequence containing at least one B-L-deoxynucleoside or 3′-deoxy nucleoside.

In certain embodiments of the invention, the immune regulatoryoligonucleotide comprises a nucleic acid sequence containing at leastone dinucleotide selected from CpG, C*pG, C*pG* and CpG*, wherein C iscytosine or 2′-deoxycytidine, G is guanosine or 2′-deoxyguanosine, C* is2′-deoxythymidine,1-(2′-deoxy-3-D-ribofuranosyl)-2-oxo-7-deaza-8-methyl-purine, 5-Me-dC,2′-dideoxy-5-halocytosine, 2′-dideoxy-5-nitrocytosine, arabinocytidine,2′-deoxy-2′-substituted arabinocytidine, 2′-O-substitutedarabinocytidine, 2′-deoxy-5-hydroxycytidine, 2′-deoxy-N4-alkyl-cytidine,2′-deoxy-4-thiouridine, 2′-O-substituted ribonucleotides (including, butnot limited to, 2′-O-Me-5-Me-C, 2′-O-(2-methoxyethyl)-ribonucelotides or2′-O-Me-ribonucleotides) or other pyrimidine nucleoside analogs orderivative, G* is 2′-deoxy-7-deazaguanosine, 2′-deoxy-6-thioguanosine,arabinoguanosine, 2′-deoxy-2′substituted-arabinoguanosine,2′-O-substituted-arabinoguanosine, 2′-deoxyinosine, 2′-O-substitutedribonucleotides (including, but not limited to,2′-O-(2-methoxyethyl)-ribonucelotides; or 2′-O-Me-ribonucleotides) orother purine nucleoside analogs or derivative, and p is aninternucleoside linkage selected from the group consisting ofphosphodiester, phosphorothioate, and phosphorodithioate, and whereinthe activity of the at least one dinucleotide is regulated by theflanking sequence.

In some embodiments, the oligonucleotides of the IRO compound each havefrom about 6 to about 35 nucleoside residues, preferably from about 9 toabout 30 nucleoside residues, more preferably from about 11 to about 23nucleoside residues. In some embodiments, the oligonucleotides have fromabout 6 to about 18 nucleotide residues.

In some embodiments, the IRO compounds can be combined with one or morevaccines, antigens, antibodies, cytotoxic agents, allergens,antibiotics, antisense oligonucleotides, TLR agonist, TLR antagonist,peptides, proteins, gene therapy vectors, DNA vaccines, adjuvants orkinase inhibitors to enhance the specificity or magnitude of the immuneresponse, or co-stimulatory molecules such as cytokines, chemokines,protein ligands, trans-activating factors, peptides and peptidescomprising modified amino acids.

In a second aspect, the invention provides a pharmaceutical compositioncomprising an IRO compound according to the invention and aphysiologically acceptable carrier.

In embodiments of this aspect of the invention, the composition canfurther comprise one or more vaccines, antigens, antibodies, cytotoxicagents, allergens, antibiotics, antisense oligonucleotides, TLR agonist,TLR antagonist, peptides, proteins, gene therapy vectors, DNA vaccines,adjuvants or kinase inhibitors to enhance the specificity or magnitudeof the immune response, or co-stimulatory molecules such as cytokines,chemokines, protein ligands, trans-activating factors, peptides andpeptides comprising modified amino acids.

In a third aspect, the invention provides methods for inhibiting orsuppressing TLR-mediated induction of an immune response in a mammal,such methods comprising administering to the mammal an IRO compoundaccording to the invention. In some embodiments, the mammal is a human.In preferred embodiments, the IRO compound is administered to a mammalin need of immune suppression.

According to this aspect of the invention, an IRO compound is capable ofsuppressing a TLR-based immune response to a further TLR ligand or TLRagonist. As discussed further in the Examples below, the activation of aTLR-based immune response by a TLR agonist or TLR ligand (for example,an immune stimulatory oligonucleotide) can be antagonized, inhibited,suppressed or prevented by the simultaneous, pre- or post-administrationof an IRO compound, and such antagonism, inhibition, suppression orprevention may be maintained for an extended period of time (forexample, days) after administration. This beneficial property of thecurrent invention has a unique advantage for the prevention and/ortreatment of a disease or disorder. For example, application of certainTLR-agonists in the course of treating the disease may cause unwantedimmune stimulation that an IRO compound could antagonize, suppress,inhibit or prevent. Administration of the IRO simultaneously, pre and/orpost administration of the TLR-agonist may allow therapeutic benefitsfrom the TLR-agonist while antagonizing, suppressing, inhibiting orpreventing the unwanted side effect(s). Additionally, pre-administrationof an IRO compound according to the invention could antagonize,suppress, inhibit or prevent an immune response (for example, anallergic reaction) to a subsequent or later challenge by a TLR-agonist.Preferably a TLR7 and/or TLR9 agonist.

In the methods according to this aspect of the invention, administrationof IRO compound according to the invention can be by any suitable route,including, without limitation, parenteral, mucosal delivery, oral,sublingual, transdermal, topical, inhalation, intragastric, intranasal,aerosol, intraocular, intratracheal, intrarectal, vaginal, by gene gun,dermal patch or in eye drop or mouthwash form. Administration of thetherapeutic compositions of IRO compound can be carried out using knownprocedures at dosages and for periods of time effective to reducesymptoms or surrogate markers of the disease. When administeredsystemically, the therapeutic composition is preferably administered ata sufficient dosage to attain a blood concentration of IRO compound fromabout 0.0001 micromolar to about 100 micromolar. More preferably,systemic administration would be at a sufficient dosage to attain ablood concentration of the IRO compound from about 0.001 micromolar toabout 10 micromolar. For localized administration, much lowerconcentrations than this may be effective, and much higherconcentrations may be tolerated. Preferably, a total dosage of IROcompound ranges from about 0.001 mg per patient per day to about 200 mgper kg body weight per day. It may be desirable to administer the IROcompound according to the invention daily, every second day, every thirdday, every fourth day, every fifth day, every sixth day or weekly. Itmay be desirable to administer simultaneously, or sequentially, atherapeutically effective amount of one or more of the IRO containingtherapeutic compositions of the invention to an individual as a singletreatment episode.

The IRO compound may optionally be linked to one or more allergensand/or antigens (self or foreign), an immunogenic protein, such askeyhole limpet hemocyanin (KLH), cholera toxin B subunit, or any otherimmunogenic carrier protein. IRO can also be used in combination withother compounds (for example, adjuvants) including, without limitation,TLR agonists (e.g. TLR2 agonists, TLR4 agonists, and TLR9 agonists),Freund's incomplete adjuvant, KLH, monophosphoryl lipid A (MPL), alum,Merck alum adjuvant (MAA), and saponins, including QS-21 and imiquimod,or combinations thereof.

The methods according to this aspect of the invention are useful formodel studies of the immune system. The methods are also useful for theprophylactic or therapeutic treatment of human or animal disease. Forexample, the methods are useful for pediatric, adult, and veterinaryvaccine applications.

In a fourth aspect, the invention provides methods for therapeuticallytreating a patient having a disease or disorder, such methods comprisingadministering to the patient a IRO compound according to the invention.In various embodiments, the disease or disorder to be treated is cancer,an autoimmune disorder, airway inflammation, inflammatory disorders,infectious disease, malaria, Lyme disease, ocular infections,conjunctivitis, skin disorders, psoriasis, scleroderma, cardiovasculardisease, atherosclerosis, chronic fatigue syndrome, sarcoidosis,transplant rejection, allergy, asthma or a disease caused by a pathogen.Preferred autoimmune disorders include without limitation lupuserythematosus, multiple sclerosis, type I diabetes mellitus, irritablebowel syndrome, Chron's disease, rheumatoid arthritis, septic shock,alopecia universalis, acute disseminated encephalomyelitis, Addison'sdisease, ankylosing spondylitis, antiphospholipid antibody syndrome,autoimmune hemolytic anemia, autoimmune hepatitis, Bullous pemphigoid,chagas disease, chronic obstructive pulmonary disease, coeliac disease,dermatomyositis, endometriosis, Goodpasture's syndrome, Graves' disease,Guillain-Barré syndrome, Hashimoto's disease, hidradenitis suppurativa,idiopathic thrombocytopenic purpura, interstitial cystitis, morphea,myasthenia gravis, narcolepsy, neuromyotonia, pemphigus, perniciousanaemia, polymyositis, primary biliary cirrhosis, schizophrenia,Sjögren's syndrome, temporal arteritis (“giant cell arteritis”),vasculitis, vitiligo, vulvodynia and Wegener's granulomatosis. Preferredinflammatory disorders include without limitation airway inflammation,asthma, autoimmune diseases, chronic inflammation, chronic prostatitis,glomerulonephritis, Behçet's disease, hypersensitivities, inflammatorybowel disease, reperfusion injury, rheumatoid arthritis, transplantrejection, ulcerative colitis, uveitis, conjunctivitis and vasculitis.Pathogens include bacteria, parasites, fungi, viruses, viroids, andprions. Administration is carried out as described for the third aspectof the invention.

In a fifth aspect, the invention provides methods for preventing adisease or disorder, such methods comprising administering to thepatient IRO compound according to the invention. In various embodiments,the disease or disorder to be prevented is cancer, an autoimmunedisorder, airway inflammation, inflammatory disorders, infectiousdisease, malaria, Lyme disease, ocular infections, conjunctivitis, skindisorders, psoriasis, scleroderma, cardiovascular disease,atherosclerosis, chronic fatigue syndrome, sarcoidosis, transplantrejection, allergy, asthma or a disease caused by a pathogen. Preferredautoimmune disorders include without limitation lupus erythematosus,multiple sclerosis, type I diabetes mellitus, irritable bowel syndrome,Chron's disease, rheumatoid arthritis, septic shock, alopeciauniversalis, acute disseminated encephalomyelitis, Addison's disease,ankylosing spondylitis, antiphospholipid antibody syndrome, autoimmunehemolytic anemia, autoimmune hepatitis, Bullous pemphigoid, chagasdisease, chronic obstructive pulmonary disease, coeliac disease,dermatomyositis, endometriosis, Goodpasture's syndrome, Graves' disease,Guillain-Barre syndrome, Hashimoto's disease, hidradenitis suppurativa,idiopathic thrombocytopenic purpura, interstitial cystitis, morphea,myasthenia gravis, narcolepsy, neuromyotonia, pemphigus, perniciousanaemia, polymyositis, primary biliary cirrhosis, schizophrenia,Sjögren's syndrome, temporal arteritis (“giant cell arteritis”),vasculitis, vitiligo, vulvodynia and Wegener's granulomatosis. Preferredinflammatory disorders include without limitation airway inflammation,asthma, autoimmune diseases, chronic inflammation, chronic prostatitis,glomerulonephritis, Behçet's disease, hypersensitivities, inflammatorybowel disease, reperfusion injury, rheumatoid arthritis, transplantrejection, ulcerative colitis, uveitis, conjunctivitis and vasculitis.Pathogens include bacteria, parasites, fungi, viruses, viroids, andprions. Administration is carried out as described for the third aspectof the invention.

In any of the methods according to the third, fourth or fifth aspect ofthe invention, the IRO compound can be administered in combination withany other agent useful for treating or preventing the disease orcondition that does not abolish the immune antagonist, inhibitory,suppression or prevention effect or activity of the IRO compound. In anyof the methods according to the invention, the agent useful for treatingor preventing the disease or condition includes, but is not limited to,one or more vaccines, antigens, antibodies, cytotoxic agents, allergens,antibiotics, antisense oligonucleotides, TLR agonist, TLR antagonist,peptides, proteins, gene therapy vectors, DNA vaccines, adjuvants orkinase inhibitors to enhance the specificity or magnitude of the immuneresponse, or co-stimulatory molecules such as cytokines, chemokines,protein ligands, trans-activating factors, peptides and peptidescomprising modified amino acids. For example, in the treatment ofcancer, it is contemplated that the IRO compound may be administered incombination with one or more chemotherapeutic compound, targetedtherapeutic agent and/or monoclonal antibody; And in preventing adisease, it is contemplated that the IRO compound may be administered incombination with one or more vaccine. Alternatively, the agent caninclude DNA vectors encoding for antigen or allergen. In theseembodiments, the IRO compounds of the invention can variously act asadjuvants and/or produce direct immune modulatory effects.

The following examples are intended to further illustrate certainexemplary embodiments of the invention and are not intended to limit thescope of the invention. For example, representative TLR-ligands areshown in the following examples, but do not limit the scope of ligandsto which the IROs of the invention act as antagonists.

Example 1 Synthesis of Oligonucleotides Containing Immune RegulatoryMoieties

All IRO compounds of the invention were synthesized according tostandard procedures (see e.g. U.S. Patent Publication No. 20040097719).

Oligonucleotides were synthesized on a 1 μM scale using an automated DNAsynthesizer (Expedite 8909; PerSeptive Biosystems, Framingham, Mass.),following standard linear synthesis or parallel synthesis procedures(see e.g. FIGS. 5 and 6 of U.S. Patent Publication No. 20040097719).

Deoxyribonucleoside phosphoramidites were obtained from (Aldrich-Sigma,St Louis, Mo.). 1′,2′-dideoxyribose phosphoramidite,propyl-1-phosphoramidite, 2-deoxyuridine phosphoramidite,1,3-bis-[5-(4,4′-dimethoxytrityl)pentylamidyl]-2-propanolphosphoramidite and methyl phosponamidite were obtained from GlenResearch (Sterling, Va.). .beta.-L-2′-deoxyribonucleosidephosphoramidite, .alpha.-2′-deoxyribonucleoside phosphoramidite,mono-DMT-glycerol phosphoramidite and di-DMT-glycerol phosphoramiditewere obtained from ChemGenes (Willmington, Mass.).(4-Aminobutyl)-1,3-propanediol phosphoramidite was obtained fromClontech (Palo Alto, Calif.). Arabinoguanosine, was obtained fromReliable Pharmaceutical (St. Louis, Mo.). Arabinoguanosinephosphoramidite was synthesized at Idera Pharmaceuticals, Inc.(Cambridge, Mass.) (Noronha et al. (2000) Biochem., 39:7050-7062).

All nucleoside phosphoramidites were characterized by ³¹P and ¹H NMRspectra. Modified nucleosides were incorporated at specific sites usingnormal coupling cycles. After synthesis, oligonucleotides weredeprotected using concentrated ammonium hydroxide and purified byreverse phase HPLC, followed by dialysis. Purified oligonucleotides assodium salt form were lyophilized prior to use. Purity was tested by CGEand MALDI-TOF MS.

Example 2 Inhibition of TLR7 and TLR9 Stimulation

C57BL/6 mice were injected s.c. at left underarm with 5 mg/kg of an IROcompound at 0 hours and 0.25 mg/kg TLR9 agonist or 10 mg/kg TLR7 agonistat 24 hours. Serum samples were taken at 2 hours after injection of theTLR9 or TLR7 agonist and IL-12 concentration was determined by ELISA.For IRO number 40, the TLR7 and TLR9 agonists were administered 72 hoursafter administration of the IRO. The results for all IROs are shown inTables 4-11. These results demonstrate that an IRO compounds accordingto the invention can inhibit TLR7 and/or TLR9 activity in vivo, and moregenerally that IRO compounds according to the invention can inhibit TLRactivation.

TABLE 4 Antagonist Activity in vivo in mice % Inhibition of% Inhibition of TLR9 agonist TLR7 agonist Oligo No.Sequences and Modification induced IL-12 induced IL-12  15′-UGUCG1TTCT-X1-TCTTG1CUGU-5′ 44.8 94.0  2 5′-UGUCG1TTC-X1-CTTG1CUGU-5′69.8 91.6  3 5′-UGUCG1TT-X1-TTG1CUGU-5′ 63.7 89.8  45′-UGUCoG1TTCTo-Z-oTCTTG1oCUGU-5′ 27.6 53.7  55′-GUCG1TTCTT-Z-TTCTTG1CUG-5′ 75.9 97.1  6 5′-UGUCG2TTCT-Z-TCTTG2CUGU-5′70.9 99.0  7 5′-UGUCG1TTCT-X4-TCTTG1CUGU-5′ 83.2 92.6  85′-UGUCG1TTC-X4-CTTG1CUGU-5′ 68.7 78.5  95′-UGUCoG1TTCTo-X4-oTCTTG1oCUGU-5′ 76.5 18.6 105′-GUCG1TTCTT-X4-TTCTTG1CUG-5′ 87.8 100 11 5′-UGUCG1TT-X4-TTG1CUGU-5′31.1 56.8 12 5′-UGUCG1TTC-X5-CTTG1CUGU-5′ 7.3 80.4 135′-UGUCG2TTC-X5-CTTG2CUGU-5′ 48.6 98.1 14 5′-UGUCG1TTC-X6-CTTG1CUGU-5′64.6 92.2 15 5′-UGUCG2TTC-X6-CTTG2CUGU-5′ 57.1 99.9 165′-UGUCG1TTCT-X7-TCTTG1CUGU-5′ 96.5 98.5 175′-UGUCG2TTCT-X7-TCTTG2CUGU-5′ 86.2 97.3 18 5′-UGUCG1TTC-X7-CTTG1CUGU-5′94.0 98.1

TABLE 5 Antagonist Activity in vivo in mice % Inhibition of% Inhibition of TLR9 agonist TLR7 agonist Oligo No.Sequences and Modification induced IL-12 induced IL12 195′-TGUCG1TTCT-X-TCTTG1CUGT-5′ 45.2 89.8 205′-CTTGUCG1TTCT-X-TCTTG1CUGTTC-5′ 74.5 77.9 215′-TTGUCG1TTC-X-CTTG1CUGTT-5′ 66.5 86.8 225′-CTTTGUCG1TTC-X-CTTG1CUGTTTC-5′ 47.5 88.9 235′-TGUCG1TTCT-X7-TCTTG1CUGT-5′ 45.4 83.6 245′-TTGUCG1TTC-X7-CTTG1CUGTT-5′ 42.5 88.3 255′-GUCG1TTCTT-Z-TTCTTG1CUG-5′ 80.4 92.3 26 5′-TGUCG1TTCA-X-ACTTG1CUGT-5′65.8 93.2

TABLE 6 Antagonist Activity in vivo in mice Oligo No.Sequences and Modification % Inhibition of TLR9 agonist induced IL-12 275′-TCTGACG1TTCT-X-TCTTG1CAGTCT-5′ 95.8 285′-TCTGACG2TTCT-X-TCTTG2CAGTCT-5′ 97.4

TABLE 7 Antagonist Activity in vivo in mice % Inhibition of TLR9% Inhibition of TLR7 Oligo No. Sequences and Modificationagonist induced IL-12 agonist induced IL12 295′-TTGUCG1TTA-X-ATTG1CUGTT-5′ 36.6 95.3 305′-CTCTGUCG1TTA-X-ATTG1CUGTCTC-5′ 22.6 91.6 315′-TGTC*GTTCT-X-TCTTGC*TGT-5′ 78.9 32 5′-TGTCGTTCT-X-TCTTGCTGT-5′ 73.433 5′-TGTC*GTTCT-X-TCTTGC*TGT-5′ 75.5 34 5′-TGTCGTTCT-X-TCTTGCTGT-5′85.8

TABLE 8 Antagonist Activity in vivo in mice Oligo No.Sequences and Modification % Inhibition of TLR9 agonist induced IL-12 355′-UGUCG1ACAT-X-TACAG1CUGU-5′ 65.1 36 5′-UGUCG1TTC-X-CTTG1CUGU-5′ 35.737 5′-UGUCG1TT-X-TTG1CUGU-5′ 26.5 38 5′-UoGUCG1TToCTo-X-oTCoTTG1CUGoU-5′6.9 39 5′-UoGoUCG1TTCTo-X-oTCTTG1CUoGoU-5′ 16.8

TABLE 9 Antagonist Activity in vivo in mice Oligo No.Sequences and Modification % Inhibition of TLR9 agonist induced IL-12 405′-UGACG1TTCT-X-TCTTG1CAGU-5′ 54.9

TABLE 10 Antagonist Activity in vivo in mice Oligo No.Sequences and Modification % Inhibition of TLR9 agonist induced IL-12 415′-UGUCG1ACAT-Z-TACAG1CUGU-5′ 86.9 42 5′-UGUCG1TTCT-Z-TCTTG1CUGU-5′ 69.643 5′-UGUCG1TTC-Z-CTTG1CUGU-5′ 60.8 44 5′-UGUCG1TT-Z-TTG1CUGU-5′ 43.8

TABLE 11 Antagonist Activity in vivo in mice % Inhibition of TLR9% Inhibition of TLR7 oligo No. Sequences and Modificationagonist induced IL-12 agonist induced IL12 58 5′-CTATCTGAC*GTTCTCTGT-3′72.6 79.8 62 5′-CTATCTG{circumflex over ( )}A{circumflex over( )}CGTTCTCTGT-3′ 68.1 30.9

TABLE 12 Antagonist Activity in vivo in mice % Inhibition of IL-12oligo No. Sequence TLR9 TLR7 71 5′-CTTTGUC*G1TTC-X-CTTG1C*UGTTTC-5′ 55.594.9 77 5′-CTTGUC*G1TTCT-X-TCTTG1C*UGTTC-5′ 71.5 92.8 785′-CTTTGUC*oG1TTC-X-CTTG1oC*UGTTTC-5′ 25.6 83.4 805′-CTTGUC*oG1TTCT-X-TCTTG1oC*UGTTC-5′ 6.7 68.2 825′-CTGUC*oG1TTCTT-X-TTCTTG1oC*UGTC-5′ 9.0 78.4 885′-CTATCTGUC*G1TTCTCTGT-3′ 63.2 77.7 89 5′-CTATCTGUC*G1TTCTCTGT-3′ 36.440.5

Example 3 TLR7/TLR9 In Vitro Antagonist Study

C57BL/6 mice were used in this study. Mouse splenocytes were culturedfor 24 hrs (at 37° C., 5% CO₂) with TLR7/TLR9 antagonists over a doserange 0.3, 1, 5, 10 mg/ml or at a single dose, 10 mg/ml in the presenceof a TLR7 agonist (200 mg/ml) or in the presence of a TLR9 agonist (1mg/ml) or in the presence of PBS. Supernatants were collected andcytokine/chemokine responses were then evaluated in supernatants bymultiplex assays using the Luminex xMAP system. Samples were assayed induplicate (+SD). Results are shown in FIGS. 3 and 4.

Example 4 TLR7/TLR9 In Vivo Antagonist Study

Female C57BL/6 mice (2/group) were s.c injected with 1, 5 or 15 mg/kgantagonist compound at 0 hr in the right flank. The mice were theninjected with TLR7 agonist (10 mg/kg) or with TLR9 agonist (0.25 mg/kg)at 24 hrs in the left flank. Blood was collected by orbital bleeding 2hrs post the agonist administration. The serum samples were thenanalyzed by IL-12 ELISA. Results are shown in FIGS. 5 and 6.

Additionally, female C57BL/6 mice (2/group) were s.c injected with 5mg/kg antagonist compound at day 0 in the right flank. The mice werethen injected with TLR7 (10 mg/kg) agonist at days 1, 2, 4, 9 and 11 orwith TLR9 (0.25 mg/kg) agonist at days 1, 2, 4, 7, 9 and 11 in the leftflank. Blood was collected by orbital bleeding 2 hrs post the agonistadministration. The serum samples were then analyzed by IL-12 ELISA.Results are shown in FIGS. 7 and 8.

Female C57BL/6 mice (2/group) were also s.c injected with 5 mg/kgantagonist compound at 0 hr in the right flank. The mice were theninjected with TLR9 (0.25 mg/kg) or TLR7 (10 mg/kg) agonists at 24 hrs inthe left flank. Blood was collected by orbital bleeding 2 hrs post theagonist administration. Cytokine/chemokine responses were then evaluatedin serum samples by multiplex assays using the Luminex xMAP system.Results are shown in FIG. 9.

Finally, female C57BL/6 mice (2/group) were s.c injected with 5 mg/kgantagonist compound at 0 hr in the right flank. The mice were theninjected with TLR3 (10 mg/kg) or TLR5 (0.25 mg/kg) agonists at 24 hrs inthe left flank. Blood was collected by orbital bleeding 2 hrs post theagonist administration. Cytokine/chemokine responses were then evaluatedin serum samples by multiplex assays using the Luminex xMAP system.Results are shown in FIG. 10.

While this invention has been particularly shown and described withreferences to preferred embodiments thereof, it will be understood bythose skilled in the art that various changes in form and details may bemade therein without departing from the scope of the inventionencompassed by the appended claims.

What is claimed is:
 1. An immune regulatory oligonucleotide (IRO)compound that is an antagonist of TLR7 and/or TLR9, selected fromcompound number 1 through compound number 67 and compound number 69through compound number
 111. 2. A pharmaceutical composition comprisingan antagonist according to claim 1 and a pharmaceutically acceptablecarrier.
 3. A method for inhibiting a TLR7- and/or TLR9-mediated immuneresponse in a mammal, the method comprising administering to the mammalan antagonist according to claim 1 or a composition thereof.
 4. Themethod according to claim 3, wherein the route of administration isparenteral, mucosal delivery, oral, sublingual, transdermal, topical,inhalation, intranasal, aerosol, intraocular, intratracheal,intrarectal, vaginal, by gene gun, dermal patch or in eye drop ormouthwash form.
 5. The method according to claim 3, wherein the mammalis a human.
 6. The method according to claim 3, wherein the antagonistis administered in combination with one or more vaccines, antigens,antibodies, cytotoxic agents, allergens, antibiotics, antisenseoligonucleotides, TLR agonists, TLR antagonists, peptides, proteins,gene therapy vectors, DNA vaccines, adjuvants, kinase inhibitors orco-stimulatory molecules.
 7. A method for inhibiting the activity of aTLR7 and/or TLR9 agonist comprising administering an antagonistaccording to claim 1 or a composition thereof.
 8. The method accordingto claim 7, comprising administering the antagonist prior to or at thesame time as the TLR7 and/or TLR9 agonist.
 9. A method fortherapeutically treating a mammal having an autoimmune disease mediatedby TLR7 and/or TLR9 or an inflammatory disease mediated by TLR7 and/orTLR9, such method comprising administering to the mammal an antagonistaccording to claim 1 or a composition thereof.
 10. The method accordingto claim 9, wherein the autoimmune disease is selected from psoriasis,lupus erythematosus, multiple sclerosis, type I diabetes mellitus,irritable bowel syndrome, Chron's disease, rheumatoid arthritis, septicshock, alopecia universalis, acute disseminated encephalomyelitis,Addison's disease, ankylosing spondylitis, antiphospholipid antibodysyndrome, autoimmune hemolytic anemia, autoimmune hepatitis, Bullouspemphigoid, chagas disease, chronic obstructive pulmonary disease,coeliac disease, dermatomyositis, endometriosis, Goodpasture's syndrome,Graves' disease, Guillain-Barré syndrome, Hashimoto's disease,hidradenitis suppurativa, idiopathic thrombocytopenic purpura,interstitial cystitis, morphea, myasthenia gravis, narcolepsy,neuromyotonia, pemphigus, pernicious anaemia, polymyositis, primarybiliary cirrhosis, schizophrenia, Sjögren's syndrome, temporalarteritis, vasculitis, vitiligo, vulvodynia, and Wegener'sgranulomatosis.
 11. The method according to claim 9, wherein theinflammatory disease is selected from airway inflammation, asthma,chronic inflammation, chronic prostatitis, glomerulonephritis, Behçet'sdisease, hypersensitivities, inflammatory bowel disease, reperfusioninjury, rheumatoid arthritis, transplant rejection, ulcerative colitis,uveitis, conjunctivitis, and vasculitis.
 12. The method according toclaim 9, wherein the antagonist is administered in combination with oneor more vaccines, antigens, antibodies, cytotoxic agents, allergens,antibiotics, antisense oligonucleotides, TLR agonists, TLR antagonists,peptides, proteins, gene therapy vectors, DNA vaccines, adjuvants,kinase inhibitors or co-stimulatory molecules.
 13. The method accordingto claim 9, wherein the route of administration is parenteral, mucosaldelivery, oral, sublingual, transdermal, topical, inhalation,intranasal, aerosol, intraocular, intratracheal, intrarectal, vaginal,by gene gun, dermal patch or in eye drop or mouthwash form.
 14. Themethod according to claim 9, wherein the mammal is a human.
 15. A methodfor preventing an autoimmune disease mediate by a TLR7 and/or TLR9 or aninflammatory disease mediated by TLR7 and/or TLR9, such methodcomprising administering to a mammal an antagonist according to claim 1or a composition thereof.
 16. The method according to claim 15, whereinthe autoimmune disease is selected from psoriasis, lupus erythematosus,multiple sclerosis, type I diabetes mellitus, irritable bowel syndrome,Chron's disease, rheumatoid arthritis, septic shock, alopeciauniversalis, acute disseminated encephalomyelitis, Addison's disease,ankylosing spondylitis, antiphospholipid antibody syndrome, autoimmunehemolytic anemia, autoimmune hepatitis, Bullous pemphigoid, chagasdisease, chronic obstructive pulmonary disease, coeliac disease,dermatomyositis, endometriosis, Goodpasture's syndrome, Graves' disease,Guillain-Barre syndrome, Hashimoto's disease, hidradenitis suppurativa,idiopathic thrombocytopenic purpura, interstitial cystitis, morphea,myasthenia gravis, narcolepsy, neuromyotonia, pemphigus, perniciousanaemia, polymyositis, primary biliary cirrhosis, schizophrenia,Sjögren's syndrome, temporal arteritis, vasculitis, vitiligo,vulvodynia, and Wegener's granulomatosis.
 17. The method according toclaim 15, wherein the inflammatory disease is selected from airwayinflammation, asthma, chronic inflammation, chronic prostatitis,glomerulonephritis, Behçet's disease, hypersensitivities, inflammatorbowel disease, reperfusion injury, rheumatoid arthritis, transplantrejection, ulcerative colitis, uveitis, conjunctivitis, and vasculitis.18. The method according to claim 15, wherein the antagonist isadministered in combination with one or more vaccines, antigens,antibodies, cytotoxic agents, allergens, antibiotics, antisenseoligonucleotides, TLR agonists, TLR antagonists, peptides, proteins,gene therapy vectors, DNA vaccines, adjuvants or co-stimulatorymolecules.
 19. The method according to claim 15, wherein the route ofadministration is parenteral, mucosal delivery, oral, sublingual,transdermal, topical, inhalation, intranasal, aerosol, intraocular,intratracheal, intrarectal, vaginal, by gene gun, dermal patch or in eyedrop or mouthwash form.
 20. The method according to claim 15, whereinthe mammal is a human.
 21. The composition according to claim 2, furthercomprising one or more vaccines, antigens, antibodies, cytotoxic agents,allergens, antibiotics, antisense oligonucleotides, TLR agonists, TLRantagonists, peptides, proteins, gene therapy vectors, DNA vaccines,adjuvants or co-stimulatory molecules.